feat(encode): add gget encode module to query and download ENCODE data (#151)#231
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Elarwei001 wants to merge 3 commits into
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feat(encode): add gget encode module to query and download ENCODE data (#151)#231Elarwei001 wants to merge 3 commits into
Elarwei001 wants to merge 3 commits into
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scverse#151) New module `gget encode` queries the ENCODE project REST API (https://www.encodeproject.org/). Passing an ENCODE accession (experiment or file) returns the matching file(s) with download URLs, optionally filtered by assembly/file_format/output_type and downloaded with download=True; any other input is used as a free-text search returning matching ENCODE objects of a given type. Exposed via the Python API and the command line. 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 #231 +/- ##
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+ Coverage 56.14% 56.92% +0.78%
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Files 29 30 +1
Lines 9244 9349 +105
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+ Hits 5190 5322 +132
+ Misses 4054 4027 -27 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Add network-free mocked tests for _encode_get error/404 branches, the output_type filter, generic-object metadata path, accession download, search-path verbose/download warning, save CSV/JSON, and the streaming _download_files body. gget_encode.py now fully covered. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Resolves #151
Summary
gget encode: New module to query and download data from the ENCODE project. Pass an ENCODE accession (e.g.ENCSR000AKSexperiment orENCFF000BXKfile) to list its file(s) with download URLs — optionally filtered byassembly,file_format, andoutput_type, and downloaded withdownload=True— or pass a free-text term to search ENCODE objects of a giventype. Available in the Python API and on the command line. Resolves issue 151.Testing
Unit tests in
tests/test_encode.pywith fixturetests/fixtures/test_encode.json; run with pytest.