openvax / pyensembl / 24854025201

84%

master: 83%

Build Type

Pull #333

github

Committed by iskandr

Commit Message

Fix #252: Transcript.coding_sequence handles missing codon features

When a protein-coding transcript in the GTF lacks a start_codon or
stop_codon feature (common in Ensembl Plants fragments and incomplete
annotations), Transcript.coding_sequence previously raised ValueError
from _transcript_feature_position_ranges. Transcript.complete
short-circuits safely via contains_start_codon / contains_stop_codon, so
.complete itself was correct — but calling .coding_sequence directly
crashed.

Return None from .coding_sequence when either the start_codon or the
stop_codon feature is absent, matching the existing "missing sequence"
behavior.

Adds a TAIR10 regression fixture (AT1G01010.1, AT1G03325.1, AT1G24475.1)
from Ensembl Plants release 57 covering a complete transcript plus the
two fragment cases. The complete-transcript test also guards the
original #252 scenario — before #268 stripped the ".N" isoform suffix
only for ENSEMBL IDs, this case would have returned False.

Pull Request Pull Request #333: Fix #252: Transcript.coding_sequence handles TAIR fragments missing start/stop codons

Coverage Stats

5 of 5 new or added lines in 2 files covered. (100.0%)

2 existing lines in 1 file now uncovered.

1346 of 1611 relevant lines covered (83.55%)

3.34 hits per line