openvax / pyensembl

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LAST BUILD ON BRANCH v2.9.7

branch: v2.9.7

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Build # 25806144871

Build Type

push

github

Committed by web-flow

Commit Message

Rename sequence_lookup_with_ens_fallback → lookup_sequence_with_version_fallback (#352)

The old name was misleading: the fallback isn't to "ENS" (both Ensembl
and GENCODE IDs start with ENS); the fallback is to a version-stripped
form. The ENS prefix is just a safety gate so we don't strip non-Ensembl
.N suffixes (e.g. TAIR isoform suffixes like AT1G01010.1).

Docstring rewritten to reflect that both Ensembl and GENCODE produce
versioned IDs - the formats just split that information differently
(Ensembl in a separate *_version attribute, GENCODE embedded in the ID
itself). The helper exists for the GENCODE case where the GTF stores
the full versioned ID and a literal FASTA lookup would miss.

No back-compat shim: this helper was added today in v2.9.6 and isn't
exposed in __init__.py, so no external callers can depend on the old
name.

Bump version to 2.9.7.

Coverage Stats

8 of 8 new or added lines in 4 files covered. (100.0%)

1600 of 1883 relevant lines covered (84.97%)

3.4 hits per line