feat(rummage): add gget rummagene and rummageo modules (#164)#230
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feat(rummage): add gget rummagene and rummageo modules (#164)#230Elarwei001 wants to merge 2 commits into
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New modules `gget rummagene` and `gget rummageo` query the public Rummagene and RummaGEO GraphQL APIs for gene set enrichment against gene sets mined from PMC supplementary tables and GEO study signatures, respectively. Submit a list of gene symbols to retrieve the most significantly overlapping gene sets (Fisher's exact test), ranked by p-value. Both functions share a single `_rummage_enrich` helper and are exposed through the Python API and the command line, with limit/filter_term/json/save options. 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 #230 +/- ##
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+ Coverage 56.14% 56.92% +0.77%
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Files 29 30 +1
Lines 9244 9327 +83
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+ Hits 5190 5309 +119
+ Misses 4054 4018 -36 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Add network-free mocked tests for the filter_term branch, verbose logging, request-exception handling, and the save-to-CSV/JSON branches, bringing gget_rummage.py to full coverage. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Resolves #164
Summary
gget rummageneandgget rummageo: New modules for gene set enrichment against gene sets automatically mined from PMC supplementary tables (Rummagene) and from GEO study signatures (RummaGEO). Submit a list of gene symbols to retrieve the most significantly overlapping literature/GEO gene sets (Fisher's exact test), ranked by p-value, via each service's public GraphQL API. Both share a single enrichment helper and support thelimit,filter_term,json, andsaveoptions in the Python API and on the command line. Resolves issue 164.Testing
Unit tests in
tests/test_rummage.pywith fixturestests/fixtures/test_rummagene.jsonandtests/fixtures/test_rummageo.json; run with pytest.