openvax / pyensembl

83%

master: 83%

LAST BUILD ON BRANCH v2.6.6

branch: v2.6.6

CHANGE BRANCH

x

Reset

• v2.6.6
• add-GRCm39
• add-fly
• comparison-on-Locus
• docs-drop-readme-line-anchors
• docs-readme-source-links
• docs-readme-text-fragment-anchors
• ensembl-115-mouse-strains
• feature-296-pyensembl-available
• feature-pretty-pyensembl-available
• feature/preserve-fasta-versions
• fix-169-extended-protein-coding-flags
• fix-176-coding-sequence-ranges-include-stop-codon
• fix-177-biotype-kwarg
• fix-186-locus-intersect
• fix-190-merged-gene-intervals
• fix-219-database-default-cache-dir
• fix-242-version-and-versioned-id
• fix-252-complete-tair
• fix-260-locus-overlap-length
• fix-280-distance-to-locus-ignore-strand
• fix-283-nearest-gene-transcript
• fix-286-protein-ids-at-locus
• fix-298-ensembl-genomes-divisions
• fix-335-part1-gencode-biotype-aliases
• fix-335-part2-versioned-protein-fasta
• fix-MT-normalization
• fix-exon-id-missing
• fix-hla-a-locus-tests
• fix-pypi-autodeploy
• fix-tsl-parentheses
• fix/coveralls-parallel
• fix/python314-argparse
• fixing-travis
• follow-up-334-soybean-xenopus-tighter-ranges
• get-rid-of-ensembl-id-checking-too-many-exceptions
• issue-287-ensembl-110
• main
• master
• max-release-100
• max-release-99
• new-ensembl-versions-96-97
• numpy2-support
• only-create-dir-if-necessary
• relax-serializable-ceiling
• remove-assert-statements
• remove-encrypted-values-for-external-contrib
• remove-pandas-dependency
• rename-version-fallback-helper
• up-max-release
• v2.10.0
• v2.10.1
• v2.3.11
• v2.3.12
• v2.3.13
• v2.3.9
• v2.6.10
• v2.6.11
• v2.6.12
• v2.6.13
• v2.6.4
• v2.6.5
• v2.6.7
• v2.6.8
• v2.6.9
• v2.7.0
• v2.8.0
• v2.9.0
• v2.9.1
• v2.9.2
• v2.9.3
• v2.9.4
• v2.9.5
• v2.9.6
• v2.9.7
• v2.9.8
• worktree-feature+update_setuptools

Build # 24727646321

Build Type

push

github

Committed by web-flow

Commit Message

Fix #176: coding_sequence_position_ranges includes stop codon (#330)

len(Transcript.coding_sequence) exceeded the total length of
coding_sequence_position_ranges by exactly 3 because Ensembl GTF writes
the stop codon as a separate "stop_codon" feature, not part of the CDS
ranges — while coding_sequence is computed from start_codon to
stop_codon spliced offsets.

Now extend coding_sequence_position_ranges to include the stop codon
positions and merge adjacent ranges, so the lengths agree. A new
_merge_ranges helper handles the typical case where the stop codon
abuts the last CDS exon.

Bumps to 2.6.6.

Coverage Stats

15 of 16 new or added lines in 2 files covered. (93.75%)

1333 of 1602 relevant lines covered (83.21%)

3.33 hits per line