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Build # 24734930296

Build Type

push

github

Committed by web-flow

Commit Message

Fix Transcript.exons on GTFs without exon_id attribute (#331)

Ensembl release 54 and some non-Ensembl GTFs (e.g. UCSC refseq/gencode)
omit the exon_id attribute. pyensembl's installer already treats the
column as optional (database.py:134), but Transcript.exons still
unconditionally SELECTed exon_id, crashing with
sqlite3.OperationalError: no such column: exon_id.

Transcript.exons now checks db.column_exists("exon", "exon_id") and
falls back to building Exon objects directly from the exon row with a
synthesized per-transcript ID of the form "<transcript_id>_exon_<n>".

Adds a regression test that builds an Ensembl-style GTF with
exon_number but no exon_id and verifies both exon ordering and
synthesized IDs.

Bumps to 2.6.7.

Coverage Stats

17 of 18 new or added lines in 2 files covered. (94.44%)

1343 of 1609 relevant lines covered (83.47%)

3.34 hits per line