feat(blast): add taxonomy/organism filtering via taxid and entrez_query (#71)#228
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…ry (scverse#71) Add `taxid` and `entrez_query` arguments to `gget blast` (Python API and CLI) so searches can be restricted by organism, mirroring the "Organism" field of the NCBI web BLAST app. `taxid` accepts a single ID or a list (combined with OR as `txid<ID>[ORGN]`); `entrez_query` passes a raw NCBI Entrez query through to `ENTREZ_QUERY`. When both are given they are AND-combined. Both default to None, preserving backward compatibility. Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
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## dev #228 +/- ##
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+ Coverage 56.14% 56.69% +0.55%
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Files 29 29
Lines 9244 9263 +19
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+ Hits 5190 5252 +62
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Resolves #71
Summary
gget blast: Added taxonomy/organism filtering via the newtaxidandentrez_queryarguments (CLI:--taxid/-taxand--entrez_query/-eq), mirroring the "Organism" field of the NCBI web BLAST app (resolves issue 71).Testing
Unit tests added/extended in
tests/test_blast.pywith fixture entries intests/fixtures/test_blast.json; run with pytest.