Files

gbanyan b63251a996 fix: resolve JOIN explosion from duplicate gene_ids across evidence tables

- 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>

2026-02-16 04:48:13 +08:00

894 B

Raw Blame History

Pipeline Reproducibility Report

Run ID: 0bcdae80-84c2-486b-809a-36040ce4821d Timestamp: 2026-02-15T20:47:54.482074+00:00 Pipeline Version: 0.1.0

Parameters

Scoring Weights:

gnomAD: 0.20
Expression: 0.20
Annotation: 0.15
Localization: 0.15
Animal Model: 0.15
Literature: 0.15

Data Versions

ensembl_release: 113
gnomad_version: v4.1
gtex_version: v8
hpa_version: 23.0

Software Environment

python: 3.14.3
polars: 1.38.1
duckdb: 1.4.4

Filtering Steps

Step	Input Count	Output Count	Criteria
load_scored_genes	0	0
apply_tier_classification	0	0
write_candidate_output	0	0
generate_visualizations	0	0

Tier Statistics

Total Candidates: 19342
HIGH: 44
MEDIUM: 7268
LOW: 12030

894 B Raw Blame History

Pipeline Reproducibility Report

Parameters

Data Versions

Software Environment

Filtering Steps

Tier Statistics

894 B

Raw Blame History