openvax / pyensembl / 25776010820

85%

master: 83%

Build Type

push

github

Committed by web-flow

Commit Message

Fix #335 (part 2): tolerate versioned IDs in protein/transcript FASTA lookups (#350)

GENCODE GTFs embed the assembly version directly in the protein_id and
transcript_id attributes (e.g. protein_id "ENSP00000123456.3"), while
pyensembl's FASTA parser strips ENS.N suffixes from headers. The literal
lookup with the versioned ID therefore missed, and Transcript.protein_sequence
returned None for GENCODE FASTAs even when the sequence was present.

Adds sequence_data.sequence_lookup_with_ens_fallback() which tries the
literal id first (handles both unversioned Ensembl GTFs and any future
FASTA that preserves versions) and falls back to the version-stripped
form for ENS.N identifiers.

Wires the helper into:
- Transcript.sequence (previously stripped unconditionally; now tries
  versioned first then strips)
- Transcript.protein_sequence (previously missing for GENCODE GTFs)
- Genome.transcript_sequence(transcript_id)
- Genome.protein_sequence(protein_id)

Bump version to 2.9.6.

Coverage Stats

16 of 18 new or added lines in 4 files covered. (88.89%)

1 existing line in 1 file now uncovered.

1600 of 1883 relevant lines covered (84.97%)

3.4 hits per line