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detect: exonerate gets the NCBI table string for codes it lacks (the commit #13/#16 missed) - #17
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…t-in table for Replaces the miniprot-only fallback: exonerate gets polished models for code 26 too. exonerate's --geneticcode also takes a 64-letter table (NCBI TCAG order); the string is built from Biopython's NCBI tables. Measured on exonerate 2.4.0: a synthetic 120-aa gene with 15 CTG codons aligns at identity 100.00 with the table-26 string, 87.50 with code 1 or 12; the 17 built-in strings equal Biopython's. Only a code with no NCBI table now skips exonerate. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya
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#13 and #16 merged only ff0e581 (skip exonerate for code 26; miniprot-only models). The table-string commit b04a77b was committed locally but never pushed, so neither PR carried it, although both descriptions describe it. This PR adds that one commit:
What it changes on main: for a genetic code exonerate has no built-in table for (24+, e.g. 26 for Alaninales), exonerate gets the 64-letter NCBI table (TCAG order, from Biopython) instead of being skipped. Only a code with no NCBI table skips exonerate.
Checks (all run on exactly this commit, frozen worktree
run-b04a77b):results/2026-10-04_regression_v061s/).results/2026-10-04_alaninales_v061_exostring/).After merge: tag
v0.6.1on this merge commit.🤖 Generated with Claude Code
Claude-Session: https://claude.ai/code/session_01JkhYFEPaa1WenE5MtA8Qya