openvax / pyensembl / 24855488254

Builds Branch Commit Type Ran Committer Via Coverage
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
83.64
24855481888 main 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
83.64
24855114232 fix-252-complete-tair Bump version to 2.6.9 Pull #333 iskandr github
83.64
24855102926 v2.6.8 Fix #297: tolerate parenthetical suffix in transcript_support_level (#332) * Fix #297: parse transcript_support_level with parenthetical suffix Recent Ensembl releases may emit values like `transcript_support_level "1 (assigned to previous versi... push web-flow github
83.52
24855090209 main Fix #297: tolerate parenthetical suffix in transcript_support_level (#332) * Fix #297: parse transcript_support_level with parenthetical suffix Recent Ensembl releases may emit values like `transcript_support_level "1 (assigned to previous versi... push web-flow github
83.52
24854921026 fix-252-complete-tair Merge 17eae8242 into a35f78777 Pull #333 web-flow github
83.59
24854918955 fix-252-complete-tair 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 r... Pull #333 iskandr github
83.59
24854817221 fix-tsl-parentheses Address review: simplify TSL split and bump to 2.6.8 Call str.split() once into `tokens` instead of twice in the ternary, and bump the version for release. Pull #332 iskandr github
83.52
24854025201 fix-252-complete-tair 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 ... Pull #333 iskandr github
83.55
24853527829 fix-tsl-parentheses Fix #297: parse transcript_support_level with parenthetical suffix Recent Ensembl releases may emit values like `transcript_support_level "1 (assigned to previous version 5)"`, causing `int(tsl)` in `Genome.transcript_by_id` to crash once gtfpars... Pull #332 iskandr github
83.51
24734930296 v2.6.7 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 T... push web-flow github
83.47
24734916651 main 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 T... push web-flow github
83.47
24733539236 fix-exon-id-missing Fix Transcript.exons on GTFs without exon_id attribute 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 Transcri... Pull #331 iskandr github
83.47
24727646321 v2.6.6 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" fe... push web-flow github
83.21
24727621145 main 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" fe... push web-flow github
83.21