From c8ecdc98df66a2b8544c2a557deb14d6285855fe Mon Sep 17 00:00:00 2001 From: Nicolai-vKuegelgen Date: Tue, 25 Jun 2024 17:02:27 +0200 Subject: [PATCH] Revert "fix: isa-tab add-ped now only modifies values on process nodes of ped supplied samples #207" This reverts commit 55f0f24c5d23035d4152ef26f3a64435bf1c4349. --- cubi_tk/isa_tab/add_ped.py | 5 - ...exome_sequencing_nucleotide_sequencing.txt | 4 - .../expected_output2/i_Investigation.txt | 95 ------------------- .../s_test_isa_tpl_add_ped.txt | 4 - tests/data/isa_tab/in_sheet_subset/input.ped | 1 - tests/test_isa_tab_add_ped.py | 24 ----- 6 files changed, 133 deletions(-) delete mode 100644 tests/data/isa_tab/expected_output2/a_test_isa_tpl_add_ped_exome_sequencing_nucleotide_sequencing.txt delete mode 100644 tests/data/isa_tab/expected_output2/i_Investigation.txt delete mode 100644 tests/data/isa_tab/expected_output2/s_test_isa_tpl_add_ped.txt delete mode 100644 tests/data/isa_tab/in_sheet_subset/input.ped diff --git a/cubi_tk/isa_tab/add_ped.py b/cubi_tk/isa_tab/add_ped.py index c5a20503..3c0334b3 100644 --- a/cubi_tk/isa_tab/add_ped.py +++ b/cubi_tk/isa_tab/add_ped.py @@ -178,9 +178,6 @@ def on_visit_material(self, material, node_path, study=None, assay=None): def on_visit_process(self, process, node_path, study=None, assay=None): super().on_visit_process(process, node_path, study, assay) - donor_name = node_path[0].name if _is_source(node_path[0]) else _sample_to_donor_name(node_path[0].name) - if donor_name not in self.donor_map: - return None proc_config_pairs = { "library construction ": { "library type": "library_type", @@ -481,8 +478,6 @@ def _append_assay_line_protocol( counter += 1 return counter, curr -def _sample_to_donor_name(sample_name): - return sample_name.rstrip("-N1") def _donor_to_sample_name(donor_name): return "%s-N1" % donor_name diff --git a/tests/data/isa_tab/expected_output2/a_test_isa_tpl_add_ped_exome_sequencing_nucleotide_sequencing.txt b/tests/data/isa_tab/expected_output2/a_test_isa_tpl_add_ped_exome_sequencing_nucleotide_sequencing.txt deleted file mode 100644 index b789a4ce..00000000 --- a/tests/data/isa_tab/expected_output2/a_test_isa_tpl_add_ped_exome_sequencing_nucleotide_sequencing.txt +++ /dev/null @@ -1,4 +0,0 @@ -Sample Name Protocol REF Parameter Value[Concentration measurement] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Provider name] Parameter Value[Provider contact] Parameter Value[Provider project ID] Parameter Value[Provider sample ID] Parameter Value[Provider QC status] Parameter Value[Requestor contact] Parameter Value[Requestor project] Parameter Value[Requestor sample ID] Parameter Value[Concentration measurement] Parameter Value[Library source] Parameter Value[Library strategy] Parameter Value[Library selection] Parameter Value[Library layout] Parameter Value[Library kit] Comment[Library kit catalogue ID] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Parameter Value[Barcode kit catalogue ID] Parameter Value[Barcode name] Parameter Value[Barcode sequence] Performer Date Library Name Characteristics[Folder name] Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Platform] Parameter Value[Instrument model] Parameter Value[Base quality encoding] Parameter Value[Center name] Parameter Value[Center contact] Performer Date Raw Data File -index-N1 Nucleic acid extraction WES index-N1-DNA1 Library construction WES GENOMIC WXS Hybrid Selection PAIRED Agilent SureSelect Human All Exon V6r2 S00000XYZ index-N1-DNA1-WES1 index Nucleic acid sequencing WES ILLUMINA Illumina NextSeq 500 Phred+33 -father-N1 Nucleic acid extraction WES father-N1-DNA1 Library construction WES GENOMIC WXS Hybrid Selection PAIRED father-N1-DNA1-WES1 father Nucleic acid sequencing WES Phred+33 -mother-N1 Nucleic acid extraction WES mother-N1-DNA1 Library construction WES GENOMIC WXS Hybrid Selection PAIRED mother-N1-DNA1-WES1 mother Nucleic acid sequencing WES Phred+33 diff --git a/tests/data/isa_tab/expected_output2/i_Investigation.txt b/tests/data/isa_tab/expected_output2/i_Investigation.txt deleted file mode 100644 index 3d80547d..00000000 --- a/tests/data/isa_tab/expected_output2/i_Investigation.txt +++ /dev/null @@ -1,95 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO -Term Source Version 48 35 10 12 570 2.8 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology -INVESTIGATION -Investigation Identifier -Investigation Title Test ISA-Tab add-ped -Investigation Description -Investigation Submission Date -Investigation Public Release Date -Comment[Created With Configuration] /path/to/isa-configurations/bih_studies/bih_germline -Comment[Last Opened With Configuration] bih_germline -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier test_isa_tpl_add_ped -Study Title Test ISA-Tab add-ped -Study Description -Comment[Study Grant Number] -Comment[Study Funding Agency] -Study Submission Date -Study Public Release Date -Study File Name s_test_isa_tpl_add_ped.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_test_isa_tpl_add_ped_exome_sequencing_nucleotide_sequencing.txt -Study Assay Measurement Type exome sequencing -Study Assay Measurement Type Term Accession Number -Study Assay Measurement Type Term Source REF -Study Assay Technology Type nucleotide sequencing -Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 -Study Assay Technology Type Term Source REF OBI -Study Assay Technology Platform Illumina -STUDY PROTOCOLS -Study Protocol Name Sample collection Nucleic acid extraction WES Library construction WES Nucleic acid sequencing WES -Study Protocol Type Sample collection Nucleic acid extraction WES Library construction WES Nucleic acid sequencing WES -Study Protocol Type Term Accession Number -Study Protocol Type Term Source REF -Study Protocol Description -Study Protocol URI -Study Protocol Version -Study Protocol Parameters Name Concentration measurement Provider project ID;Library source;Library selection;Library layout;Barcode sequence;Wet-lab insert size;Requestor contact;Library kit;Barcode name;Provider contact;Concentration measurement;Provider sample ID;Target insert size;Provider name;Requestor project;Requestor sample ID;Barcode kit;Barcode kit catalogue ID;Provider QC status;Library strategy Base quality encoding;Platform;Center contact;Instrument model;Center name -Study Protocol Parameters Name Term Accession Number ;;;;;;;;;;;;;;;;;;; ;;;; -Study Protocol Parameters Name Term Source REF ;;;;;;;;;;;;;;;;;;; ;;;; -Study Protocol Components Name -Study Protocol Components Type -Study Protocol Components Type Term Accession Number -Study Protocol Components Type Term Source REF -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/tests/data/isa_tab/expected_output2/s_test_isa_tpl_add_ped.txt b/tests/data/isa_tab/expected_output2/s_test_isa_tpl_add_ped.txt deleted file mode 100644 index b6de4b78..00000000 --- a/tests/data/isa_tab/expected_output2/s_test_isa_tpl_add_ped.txt +++ /dev/null @@ -1,4 +0,0 @@ -Source Name Characteristics[UUID] Characteristics[External links] Characteristics[Batch] Characteristics[Family] Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Mother] Characteristics[Father] Comment[Family notes] Characteristics[Sex] Characteristics[Disease status] Characteristics[OMIM disease] Term Source REF Term Accession Number Characteristics[Orphanet disease] Term Source REF Term Accession Number Characteristics[HPO terms] Term Source REF Term Accession Number Comment[Disease notes] Protocol REF Performer Sample Name Characteristics[External links] Characteristics[Cell origin] Term Source REF Term Accession Number Characteristics[Cell type] Term Source REF Term Accession Number -index x-charite-medgen-blood-book-id:index 3 FAM_index Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 mother father female affected Sample collection index-N1 -father x-charite-medgen-blood-book-id:father . FAM_index Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 0 0 male unaffected Sample collection father-N1 -mother x-charite-medgen-blood-book-id:mother . FAM_index Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 0 0 female unaffected Sample collection mother-N1 diff --git a/tests/data/isa_tab/in_sheet_subset/input.ped b/tests/data/isa_tab/in_sheet_subset/input.ped deleted file mode 100644 index b44d7f4e..00000000 --- a/tests/data/isa_tab/in_sheet_subset/input.ped +++ /dev/null @@ -1 +0,0 @@ -FAM index father mother 2 2 diff --git a/tests/test_isa_tab_add_ped.py b/tests/test_isa_tab_add_ped.py index 9a57dec7..478c79f7 100644 --- a/tests/test_isa_tab_add_ped.py +++ b/tests/test_isa_tab_add_ped.py @@ -100,27 +100,3 @@ def test_add_ped_just_update(tmpdir): str(scratch_dir), str(pathlib.Path(__file__).parent / "data" / "isa_tab" / "expected_output"), ) - -def test_add_ped_sheet_subset_update(tmpdir): - """Test updating study and assay, but only a subset of the sheet.""" - scratch_dir = tmpdir / "scratch" - path_ped = pathlib.Path(__file__).parent / "data" / "isa_tab" / "in_sheet_subset" / "input.ped" - shutil.copytree( - str(pathlib.Path(__file__).parent / "data" / "isa_tab" / "in_just_update"), str(scratch_dir) - ) - - # Update metadata - args = BASE_ARGS[:] - args[12] = "S00000XYZ" - - argv = args + [str(scratch_dir / "i_Investigation.txt"), str(path_ped)] - - # Actually exercise code and perform test. - res = main(argv) - - assert not res - - compare_input_output( - str(scratch_dir), - str(pathlib.Path(__file__).parent / "data" / "isa_tab" / "expected_output2"), - )