Fix CTG assignment in genetic code tables 27-30 - #939
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NCBI gc.prt v4.3 changed CTG to Leu in genetic codes 27, 28, 29 and 30. The bundled table is a snapshot of gc.prt v4.2, so translate() returned Ala for these four codes. Add a test covering the CTG assignment, with controls for the tables that genuinely reassign CTG (3, 12 and 26).
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codon_tables.txtmapsCTGto Ala in genetic codes 27-30 (Karyorelict, Condylostoma, Mesodinium, Peritrich Nuclear). NCBI maps it to Leu, sotranslate()silently returns a wrong amino acid:This was never biotite's own choice. The file is a faithful snapshot of NCBI
gc.prtv4.2, added in Nov 2017 and untouched since. NCBI corrected it themselves in v4.3: "Change to CTG -> Leu in genetic codes 27, 28, 29, 30."Verification. I diffed all 64 codons of all 25 tables against
gc.prt(16,444 bytes, Version 4.6, sha2562aecbdd0…): of 1,600 assignments, exactly these 4 differ. Confirmed independently against NCBI's Taxonomy page and Biopython. Structurally, codes 27-30 reassign only stop codons, yet their leucine box readsLLLA.Deliberately left out, as a different class of change — happy to follow up if you want them: the
GTGstart missing from code 3 (gc.prt v4.4); code 24 named "Pterobranchia", which NCBI renamed "Rhabdopleuridae" (v4.6, and renaming would breakCodonTable.load("Pterobranchia Mitochondrial")); codes 32/33 absent.Tests. Table contents had no coverage: forcing
CTG -> Leuin every table left the whole suite green. The new controls (3→Thr, 12→Ser, 26→Ala — correct, and unchanged here) catch that. 6053 passed, 132 skipped; ruff 0.9.7 clean.