gbanyan
b63251a996
- scoring/integration.py: Use CTEs with GROUP BY gene_id to deduplicate all evidence tables before LEFT JOIN (gnomAD had 211K rows for 18K genes due to per-transcript data; annotation/localization also had dupes) - literature/transform.py: Deduplicate gene_symbols before PubMed queries to avoid querying the same symbol multiple times - evidence_cmd.py: Fix Polars .alias() error in literature summary display - Updated report results with full 6-layer scoring (44 HIGH, 7268 MEDIUM) - Validation PASSED: known Usher genes median percentile 86.9% 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": "0bcdae80-84c2-486b-809a-36040ce4821d",
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"timestamp": "2026-02-15T20:47:54.482074+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": 19342,
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"high": 44,
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"medium": 7268,
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"low": 12030
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}
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} |