openvax / pyensembl
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LAST BUILD ON BRANCH v2.6.9
branch: v2.6.9
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coverage: 83.642% (+0.1%) from 83.519%
24855488254

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

* 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.

* Address review: extend None-return to UTR accessors

Transcript.five_prime_utr_sequence and Transcript.three_prime_utr_sequence
shared the ValueError crash with coding_sequence when the transcript
lacked a start_codon or stop_codon feature (same root cause — direct
calls to first_start_codon_spliced_offset / last_stop_codon_spliced_offset
fall through to _transcript_feature_position_ranges with required=True).
Return None from each accessor when the relevant codon feature is absent.

Extend the TAIR10 fixture with AT1G42615.1 (neither start_codon nor
stop_codon) and add assertions covering the 5'/3' UTR accessors on all
four fragment configurations, plus a UTR+CDS round-trip on the complete
transcript.

* Bump version to 2.6.9

7 of 7 new or added lines in 2 files covered. (100.0%)

1355 of 1620 relevant lines covered (83.64%)

3.35 hits per line

Relevant lines Covered
1620 RELEVANT LINES 1355 COVERED LINES
3.35 HITS PER LINE
Source Files on v2.6.9

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24855488254 v2.6.9 Fix #252: Transcript.coding_sequence handles TAIR fragments missing start/stop codons (#333) * Fix #252: Transcript.coding_sequence handles missing codon features When a protein-coding transcript in the GTF lacks a start_codon or stop_codon feat... push web-flow github
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