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>
46 lines
894 B
Markdown
46 lines
894 B
Markdown
# Pipeline Reproducibility Report
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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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**Scoring Weights:**
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- gnomAD: 0.20
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- Expression: 0.20
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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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## 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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## 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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## Filtering Steps
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| Step | Input Count | Output Count | Criteria |
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|------|-------------|--------------|----------|
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| load_scored_genes | 0 | 0 | |
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| apply_tier_classification | 0 | 0 | |
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| write_candidate_output | 0 | 0 | |
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| generate_visualizations | 0 | 0 | |
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## Tier Statistics
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- **Total Candidates:** 19342
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- **HIGH:** 44
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- **MEDIUM:** 7268
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- **LOW:** 12030
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