Warn on ambiguous gene name lookup (2.1.1) - #46
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make_index() only checked gene.id collisions, and even that check was buggy -- it tested gene.id against the combined id+name index rather than ids alone. Gene *name* collisions (common in real annotation: paralogs, duplicated symbols) were completely silent, with the second gene silently overwriting the first in the name-based index. Track id and name collisions separately with distinct warnings: id collisions are a real anomaly (ids should be unique), name collisions are expected and just need a heads-up that lookup-by-name is ambiguous. Closes #27.
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Summary
Closes #27:
Transcriptome[...]gene lookup by name silently returned an arbitrary gene when the name was shared by multiple genes -- no warning at all.make_index()only checkedgene.idcollisions, and even that check was buggy: it testedgene.id in idx, whereidxis the combined id+name index, not an id-only set -- so it could miss real id collisions or false-positive on an id/name cross-match. Gene name collisions (expected in real annotation: paralogs, duplicated symbols) were completely unchecked.Fix tracks id and name collisions independently, each with its own warning:
Test plan
pytestsuite passes (21 passed), including a new regression test covering both id and name collision warningsflake8/blackcleanpython -m build+twine check dist/*pass at 2.1.1