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feat(data-pipelines): update lof curation pipeline with new CSVs #1573

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Jun 21, 2024
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feat(data-pipelines): update lof curation pipeline with new CSVs #1573

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0222e80
feat(data-pipelines): add new LoF curation csvs to pipeline input
rileyhgrant Jun 17, 2024
d70a4d8
refactor(graphql-api): reuse index definition in lof curation queries
rileyhgrant Jun 17, 2024
115203a
chore(browser): remove note about name and logo from policies
rileyhgrant Jun 21, 2024
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2 changes: 2 additions & 0 deletions data-pipeline/src/data_pipeline/datasets/gnomad_v2/gnomad_v2_lof_curation.py
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Expand Up @@ -22,6 +22,8 @@
"conflicting_evidence": "Uncertain",
"insufficient_evidence": "Uncertain",
"uncertain": "Uncertain",
"uncertain_lof": "Uncertain",
"likey_lof": "Likely LoF",
"likely_lof": "Likely LoF",
"likely_not_lof": "Likely not LoF",
"lof": "LoF",
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2 changes: 1 addition & 1 deletion data-pipeline/src/data_pipeline/pipelines/genes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@
"prepare_gnomad_v4_constraint",
prepare_gnomad_v4_constraint,
f"/{constraint_subdir}/gnomad_v4_constraint.ht",
{"path": "gs://gcp-public-data--gnomad/release/v4.1/constraint/gnomad.v4.1.constraint_metrics.ht"},
{"path": "gs://gcp-public-data--gnomad/release/4.1/constraint/gnomad.v4.1.constraint_metrics.ht"},
)

pipeline.add_task(
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24 changes: 24 additions & 0 deletions data-pipeline/src/data_pipeline/pipelines/gnomad_v2_lof_curation_results.py
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Expand Up @@ -16,6 +16,30 @@
# If a result for a variant/gene pair is present in more than one file,
# the result in the first file in this list takes precedence.
"curation_result_paths": [
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/ABCC8_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/ADA2_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/CBS_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/CFTR_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/EYS_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/GAMT_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/GBE1_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/HADH_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/HPS1_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/HPS3_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/HPS4_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/MFSD8_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/PCDH15_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/PLA2G6_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/POLR3A_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/POLR3B_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/POMGNT1_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/SEPN1_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/SLC13A5_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/SMARCB1_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/SMC3_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/TANGO2_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/WWOX_final_results_gnomAD.csv",
"gs://gnomad-v4-data-pipeline/inputs/lof_curation/gnomAD_v2/gnomAD_chets_final_results_gnomAD.csv",
"gs://gcp-public-data--gnomad/truth-sets/source/lof-curation/NSD1_curation_results.csv",
"gs://gcp-public-data--gnomad/truth-sets/source/lof-curation/gnomAD_addendum_curation_results.csv",
"gs://gcp-public-data--gnomad/truth-sets/source/lof-curation/metabolic_conditions_genes_curation_results.csv",
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8 changes: 5 additions & 3 deletions graphql-api/src/queries/lof-curation-result-queries.ts
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@@ -1,10 +1,12 @@
const GNOMAD_V2_LOF_CURATION_RESULTS_INDEX = 'gnomad_v2_lof_curation_results'

// ================================================================================================
// Variant query
// ================================================================================================

export const fetchLofCurationResultsByVariant = async (esClient: any, variantId: any) => {
const response = await esClient.search({
index: 'gnomad_v2_lof_curation_results',
index: GNOMAD_V2_LOF_CURATION_RESULTS_INDEX,
type: '_doc',
body: {
query: {
Expand All @@ -29,7 +31,7 @@ export const fetchLofCurationResultsByVariant = async (esClient: any, variantId:

export const fetchLofCurationResultsByGene = async (esClient: any, gene: any) => {
const response = await esClient.search({
index: 'gnomad_v2_lof_curation_results',
index: GNOMAD_V2_LOF_CURATION_RESULTS_INDEX,
type: '_doc',
size: 1000,
body: {
Expand All @@ -54,7 +56,7 @@ export const fetchLofCurationResultsByGene = async (esClient: any, gene: any) =>

export const fetchLofCurationResultsByRegion = async (esClient: any, region: any) => {
const response = await esClient.search({
index: 'gnomad_v2_lof_curation_results',
index: GNOMAD_V2_LOF_CURATION_RESULTS_INDEX,
type: '_doc',
size: 1000,
body: {
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