feat(ref): support fetching GENCODE GTFs and FASTAs (#73)#238
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Elarwei001 wants to merge 3 commits into
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feat(ref): support fetching GENCODE GTFs and FASTAs (#73)#238Elarwei001 wants to merge 3 commits into
Elarwei001 wants to merge 3 commits into
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Add a `source` argument to `gget ref` (Python API and CLI) to select the reference database: "ensembl" (default, unchanged) or "gencode" (human and mouse only). - With source="gencode", `release` is the GENCODE release number (mouse "M" prefix added automatically) and defaults to the latest release. - `which` supports gtf, dna (primary assembly genome), cdna (transcripts), ncrna (lncRNA transcripts) and pep (translations); cds is not provided by GENCODE and raises a clear error. - Returns the same dict/list structure as the Ensembl path (with a `gencode_release` field). Tests + fixtures (live GENCODE FTP) and docs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## dev #238 +/- ##
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+ Coverage 56.14% 56.51% +0.37%
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Files 29 29
Lines 9244 9321 +77
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+ Hits 5190 5268 +78
+ Misses 4054 4053 -1 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Add a network-free TestGencodeRefOffline class that mocks requests and find_FTP_link to cover _find_latest_gencode_release (human/mouse release resolution and error paths) and _gencode_ref (species and 'which' validation, link found/not-found, ftp/json save, release resolution), plus the ref() source validation and GENCODE delegation. All PR-added lines are now covered. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Resolves #73
Summary
gget ref: Added support for fetching reference GTFs and FASTAs from GENCODE (fixes issue 73).Testing
Argument-level unit tests added via fixture entries in
tests/fixtures/test_ref.json(drivingtests/test_ref.py); run with pytest.