gbanyan
fe8e13c1a1
Three bugs prevented gnomAD and expression data from contributing to scores: 1. gnomAD COLUMN_VARIANTS mapped "gene" (HGNC symbol) to gene_id instead of gene_symbol, causing JOIN miss with gene_universe (Ensembl IDs) 2. Expression HPA data was fetched but never merged (lf_hpa unused) 3. GTEx versioned Ensembl IDs (ENSG*.5) didn't match gene_universe Results: gnomAD 78.5% coverage, expression 87.4%, 19946 genes with ≥4 layers. HIGH tier refined from 44 → 18 candidates. Validation PASSED (CDH23 96.5th pctl). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
57 lines
1.2 KiB
JSON
57 lines
1.2 KiB
JSON
{
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"run_id": "e7486ff1-f9be-403b-a68d-115fc845f4a1",
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"timestamp": "2026-02-15T21:13:12.288563+00:00",
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"pipeline_version": "0.1.0",
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"parameters": {
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"gnomad": 0.2,
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"expression": 0.2,
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"annotation": 0.15,
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"localization": 0.15,
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"animal_model": 0.15,
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"literature": 0.15
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},
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"data_versions": {
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"ensembl_release": 113,
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"gnomad_version": "v4.1",
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"gtex_version": "v8",
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"hpa_version": "23.0"
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},
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"software_environment": {
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"python": "3.14.3",
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"polars": "1.38.1",
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"duckdb": "1.4.4"
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},
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"filtering_steps": [
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{
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"step_name": "load_scored_genes",
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"input_count": 0,
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"output_count": 0,
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"criteria": ""
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},
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{
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"step_name": "apply_tier_classification",
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"input_count": 0,
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"output_count": 0,
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"criteria": ""
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},
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{
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"step_name": "write_candidate_output",
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"input_count": 0,
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"output_count": 0,
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"criteria": ""
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},
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{
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"step_name": "generate_visualizations",
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"input_count": 0,
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"output_count": 0,
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"criteria": ""
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}
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],
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"validation_metrics": {},
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"tier_statistics": {
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"total": 21103,
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"high": 18,
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"medium": 9577,
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"low": 11508
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}
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} |