generate from homologs with hf#9
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samirchar
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Apr 28, 2025
samirchar
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- Created a new script to generate from homologs with hf based on query_from_homologs.
- New script lets users specify a pattern for msa files or a list of file names. Also included argumets to avoid hardcoding, like msa min seqs msa, max seqs msa, max sequence length
- For tracking left query_from_homologs untouched and moved to analysis
| parser.add_argument("--include-pattern", type=str, default="*", help="glob pattern for MSA files to include from the directory.") | ||
| parser.add_argument("--msa-file-names",nargs='*', type=str, default=None, help="List of MSA file names to include.") | ||
| parser.add_argument("--max-length", type=int, default=768, help="The maximum length of the generated text.") | ||
| parser.add_argument("--max-seqs-msa", type=int, default=57, help="The maximum number of sequences in an MSA.") |
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does the max test msa contain 57 sequences, or should this default to 64?
same q about min
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I used the hard-coded values Kevin had in the original query from homologue script here: https://github.com/microsoft/dayhoff/blob/main/analysis/query_from_homologs.py
If these are incorrect, let me know and I can change them
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noted - will look into this
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