feat: variant page — reverse lookup (genes/tissues a variant is an eQTL for) (#6)#34
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feat: variant page — reverse lookup (genes/tissues a variant is an eQTL for) (#6)#34boxiangliu wants to merge 1 commit into
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…TL for) (#6) Closes #6. No schema change (see #31): resolve the rsID's chromosome, then query the existing (chrom, rs_id) composite index. - repository.py: variant_chrom() (resolves chromosome via the SNP_A-indexed 1000G LD tables), eqtls_for_variant() (fast `WHERE chrom AND rs_id` fan-out), gene_by_id() (reverse gencode lookup, reconstructs the zero-padded ENSG). - web.py: GET /variant/{rsid} (reverse lookup, significant first, links each gene to its page); /search now routes rsIDs here. - templates/variant.html. - 100% coverage; verified live: rs62062621 -> chr17 -> 2485 associations / 119 genes across 25 tissues in ~3.5s. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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What
Closes #6. A variant page: type an rsID → see every gene × tissue where it's an eQTL (the mirror of the gene page).
/searchnow routes rsIDs here.How — and why no schema change (#31)
The reverse lookup needs the chromosome to use the
(chrom, rs_id)composite index (a barers_idfull-scans 138M rows → timeout). So:variant_chrom(rs_id)resolves the chromosome by scanning the SNP_A-indexed 1000G LD tables (autosomes) — no external service, no DDL.eqtls_for_variant(chrom, rs_id, …)then doesWHERE chrom = C AND rs_id = Xper shard — a ~100-row index seek, not a scan.gene_by_idreverse-resolves gene symbols (reconstructs the zero-padded ENSG).Results sorted most-significant-first; each gene links to its gene page.
Testing
ruff/mypy --strict/ 100% coverage (hermetic). Verified live (read-only):rs62062621→ chr17 (1.8s) → 2,485 associations across 25 tissues / 119 genes (1.7s) → HTTP 200.Notes for review
templates/variant.html(a new file — doesn't touch your in-flight gene-page redesign).repository.py/web.pynear feat: regional-plot backend (cis_associations, ld_r2, JSON endpoints) #25 and feat: CSV/TSV download of a gene's eQTL table (#7) #33 → minor merge conflicts possible if those land first; straightforward to resolve.