Repository navigation
Re-land #13 on main: exonerate NCBI table string for codes it lacks (v0.6.1) - #16
Merged
Merged
Conversation
exonerate 2.4.0 has NCBI tables 1-6, 9-16 and 21-23. For code 26 (Alaninales, CUG = Ala) it exits 1, and _run_checked made that fatal for the whole genome: 20 of 19,415 BFD Ascomycota genomes got no report in the v0.6.0 run. Exonerate is now skipped for such codes; the gene model comes from miniprot alone (polished_single). miniprot 0.18 -T 26 translates CTG as Ala (synthetic gene, 15 CTG in 120 aa: identity 1.00 with -T 26, 0.875 with -T 1 or -T 12). Version 0.6.1 (pyproject, CITATION.cff, README, CHANGELOG). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
#13 was merged into
release-builds(its stacked base) 13 s after #12 had already mergedrelease-buildsintomain, so the fix never reachedmain(main is still 0.6.0, merge commit 83aeeb0 lives only onrelease-builds). This PR brings the same two commits tomain:No new changes. Checks from #13 still apply: 1007 tests; regression vs v0.6.0 0 changed loci; Alaninales 15/20 called. After merge: tag
v0.6.1.🤖 Generated with Claude Code
Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya