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Add soulcap-match CLI and soulcap-hgnc gene-symbol mapping - #16
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…profiles Takes the four SOULCAP marker columns (required/ideal exclusions and phenotypic markers) plus --parent and --subset name hints, scores every CL term in cl_pro_relationships.tsv by marker matches/contradictions/gaps, and returns ranked candidates. Name hints add a small label-match bonus to break ties. 201 tests passing, 93.8 percent coverage. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds hgnc_id and hgnc_symbol columns to reports/cl_pro_relationships.tsv by querying the Monarch Node Normalizer (nodenormalization-sri.renci.org) with UniProtKB CURIEs (primary) and PR CURIEs as fallback for rows missing a human UniProt ID. 239/295 unique PR markers resolved to HGNC on first run; 56 blanks are isoform-specific accessions or mouse-only proteins. 236 tests passing, 94% coverage. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
This was referenced Sep 29, 2026
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Summary
Part of splitting
Alzion_G_717into small PRs (this is step 4 of the plan; #15 is step 3).soulcap-match(cl_match.py) — takes the four SOULCAP marker columns (required/ideal exclusions and phenotypic markers) plus--parent/--subsetname hints, scores every CL term incl_pro_relationships.tsvby marker matches / contradictions / gaps, and returns ranked candidates. Name hints only add a small label-match bonus to break ties.soulcap-hgnc(hgnc_map.py) — addshgnc_idandhgnc_symbolcolumns toreports/cl_pro_relationships.tsvvia the Monarch Node Normalizer, using UniProtKB CURIEs first and PR CURIEs as fallback. 239/295 unique PR markers resolved; the blanks are isoform-specific accessions or mouse-only proteins (the isoform case is fixed in a later PR).Note on the diff size: the large
reports/cl_pro_relationships.tsvchange (~9k lines) is the regenerated report gaining the two HGNC columns, not hand edits. The code iscl_match.py+hgnc_map.py(~760 lines) and their tests (~900 lines).Test plan
Verified in isolation in a separate worktree with the same steps as CI (
uv sync --frozen --extra dev):uv run pytest— 236 passed, 94.18% coverage (gate 80%)uv run ruff check .andruff format --check .passuv run mypy src/soulcap_cl_mappingpasses🤖 Generated with Claude Code