feat(ucsc): add gget ucsc module to fetch UCSC IDs (#18)#233
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feat(ucsc): add gget ucsc module to fetch UCSC IDs (#18)#233Elarwei001 wants to merge 2 commits into
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New module `gget ucsc` searches the UCSC Genome Browser REST API for a gene symbol, accession, or term and returns the matching UCSC identifiers (e.g. known gene / transcript IDs) with their genomic positions, grouped by track — analogous to gget search for Ensembl. Supports filtering by genome, track, and limit. Exposed via the Python API and the command line. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #233 +/- ##
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+ Coverage 56.14% 56.49% +0.34%
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Files 29 30 +1
Lines 9244 9320 +76
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+ Hits 5190 5265 +75
- Misses 4054 4055 +1 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Add network-free mocked tests for empty search_term, _parse_position no-range branch, verbose logging, request-exception handling, and the save CSV/JSON branches. gget_ucsc.py now 100%. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Resolves #18
Summary
gget ucsc: New module to fetch UCSC Genome Browser IDs for a gene or term, analogous togget searchfor Ensembl. Searches the UCSC Genome Browser for a symbol/accession/term and returns the matching identifiers (e.g. UCSC known gene / transcript IDs) with their genomic positions, grouped by track; supports filtering bygenome,track, andlimit. Available in the Python API and on the command line. Resolves issue 18.Testing
Unit tests in
tests/test_ucsc.pywith fixturetests/fixtures/test_ucsc.json; run with pytest.