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detect: give exonerate the NCBI table string for genetic codes it lacks (v0.6.1) - #13
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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
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run-b04a77b (PR #13): 20/20 reports, 15/20 called vs 4/20 miniprot-only; median 457 s vs 34 s per genome. Regression vs v0.6.0: 0 changed loci. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya
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Re-land #13 on main: exonerate NCBI table string for codes it lacks (v0.6.1)
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Problem
exonerate 2.4.0 has built-in NCBI tables 1–6, 9–16 and 21–23 only. For code 26 (Pachysolen tannophilus nuclear, CUG = Ala; the Alaninales) it exits 1 with
No built in genetic code corresponding to id [26]._run_checkedmakes that fatal, so the whole genome got no report: 20 of 19,415 BFD Ascomycota genomes in the v0.6.0 run.Fix
--geneticcodeas a 64-letter table in NCBI TCAG order. For a code it has no built-in table for, MATPredict now passes that string, built from Biopython's NCBI tables (ncbi_code_string,exonerate_gencode_args). No exonerate change is needed.Checks
-T 26).run-b04a77bvs v0.6.0: 0 changed loci in all five panels (results/2026-10-04_regression_v061s/).phylum_fallback(no Alaninales record), so family labels there are not reliable. Results in results: MAT campaigns — Mucoromycotina publication set; full Basidiomycota and Ascomycota on v0.6.0 #14.Stacked on #12 (
release-builds), which is stacked on #11. Merge #11, #12, then this, then tagv0.6.1.🤖 Generated with Claude Code
Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya