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Decode A3M multiple sequence alignments (0.8.0) - #8
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The MSA format ColabFold and the MMseqs2 server write and AlphaFold, Boltz, Chai, Protenix and OpenFold read. Reports the query name and length, the depth within a 4 MiB read with truncated when the file goes on, ColabFold's # chain lengths and cardinalities, mean query coverage, rows with insertions, rows whose aligned length does not fit the query, HH-suite annotation rows, the hits' source databases and the first hit's header. The server's NUL-separated multi-query files list every query. Agrees with an independent parse on 188 real files from ColabFold, Protenix, Boltz, OpenFold3 and jackhmmer; 3000 mutants never raise.
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Adds an A3M decoder: the MSA format ColabFold and the MMseqs2 server write and AlphaFold, Boltz, Chai, Protenix and OpenFold read. Neither this library nor scigantic-edge read it before.
Fields: query name and length, depth within a 4 MiB read with
truncatedwhen the file goes on, ColabFold's#chain lengths and cardinalities, mean query coverage, rows with insertions, rows whose aligned length does not fit the query (an un-realigned or mis-staged MSA), HH-suitess_pred/ss_confannotation rows, the databases the hits came from (UniRef, UniProtKB, UniParc, MGnify, SRA), the first hit's header, and every query of the server's NUL-separated multi-query files.Verification: agrees with an independent regex parse on 188 real
.a3mfiles on hand (ColabFold server output, Protenix pairing and non-pairing MSAs including two over 4 MiB, Boltz and OpenFold3 examples, jackhmmer UniRef90 / BFD / MGnify hits, an RNA alignment) on depth, query length, coverage and mismatches. The one file with mismatches is OpenFold3's deliberately un-realigned fixture. 3000 mutants of real files never raise. The scigantic-edge port is in Scigantic/scigantic-edge and was compared whole-JSON against this decoder on the same 188 files: identical.Version 0.8.0.