gbanyan
a228a56984
gene_universe contains 1,539 gene_symbols mapping to multiple Ensembl IDs (3,033 excess). Non-canonical IDs lack data in some evidence tables, causing weighted_sum/available_weight to inflate their composite scores. Fix: after scoring SQL, keep one row per gene_symbol with the most evidence_count (tiebreak by composite_score DESC). 22,604 → 19,555 genes. Results: HIGH 82→4, all top 20 now have 5-6 layers with expression data. Validation PASSED (CDH23 98.3rd percentile, median known gene 83.3%). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
46 lines
893 B
Markdown
46 lines
893 B
Markdown
# Pipeline Reproducibility Report
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**Run ID:** `f5587e39-163b-418c-8ac2-593b47323f34`
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**Timestamp:** 2026-02-16T01:59:18.969516+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:** 18243
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- **HIGH:** 4
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- **MEDIUM:** 8051
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- **LOW:** 10188
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