feat(alphafold): accept a user-provided custom MSA input (#52)#235
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Add an `msa` parameter (Python) / -msa, --msa flag (CLI) to gget alphafold that lets users supply a custom multiple sequence alignment (a3m or aligned FASTA) instead of running the internal jackhmmer search. The first sequence in the MSA must be the query. When a custom MSA is provided, gget skips the jackhmmer search and the genetic-database download entirely and builds the MSA features directly from the file. New helpers detect_msa_format()/parse_custom_msa()/ read_custom_msa() handle format detection and a3m/FASTA parsing (lowercase a3m insertions are folded into the deletion matrix, matching AlphaFold's own parser). Currently supported for single-sequence (monomer) predictions; clear errors are raised otherwise. Default behavior is unchanged (backward compatible). Resolves scverse#52. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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## dev #235 +/- ##
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+ Coverage 56.14% 56.45% +0.31%
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Files 29 29
Lines 9244 9317 +73
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Resolves #52
Summary
gget alphafold: Added a newmsaargument (-msa/--msaon the command line) that lets you provide a custom multiple sequence alignment (a3m or aligned FASTA) instead of running the internal jackhmmer search. The first sequence in the MSA must be the query. This enables folding from a manually curated MSA and skips the genetic database download entirely (currently supported for single-sequence/monomer predictions). Resolves issue 52.Testing
Unit tests in
tests/test_alphafold.pywith a3m/FASTA fixtures intests/fixtures/(parsing/validation level, since AlphaFold's heavy deps are unavailable in CI); run with pytest.