Fix #177: push biotype filter into SQL for genes() / transcripts()#344
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Genome.genes(), Genome.transcripts(), gene_ids(), transcript_ids(), and
the underlying Database.query_feature_values() now take an optional
biotype= kwarg that filters on the matching {feature}_biotype column
inside the SQL query, avoiding a Python-side scan over every feature.
Filtering by biotype on a feature whose biotype column doesn't exist
(e.g. exons) raises ValueError rather than silently returning all rows.
Bump version to 2.9.1.
|
coverage: 84.599% (+0.2%) from 84.385% — fix-177-biotype-kwarg into main |
This was referenced May 12, 2026
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Summary
Genome.genes(),Genome.transcripts(),gene_ids(),transcript_ids(), and the underlyingDatabase.query_feature_values()now accept abiotype=kwarg that is pushed into the SQL query against the{feature}_biotypecolumn.ValueErrorinstead of silently returning everything.contig/strandfilters.Closes #177.
Test plan
tests/test_biotype_filter.pycovers transcripts/genes filtered by biotype, combined contig+strand+biotype, empty-result biotype, and the no-biotype-column error pathpytest tests/test_biotype_filter.py tests/test_mouse.py tests/test_tair10_complete.py tests/test_versions.py tests/test_serialization.py(41 passed locally)./lint.shBumps version to 2.9.1.