Fix12 Add protein names to output CSV and print MAVISp-ready protein list #53
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mtiberti
requested changes
Jan 26, 2026
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| parser.add_argument("--protein-col", default="Protein", help="Column name for protein names in input CSV (default: Protein)") | ||
| parser.add_argument("--uniprot-col", default="Uniprot AC", help="Column name for UniProt IDs in input CSV (default: Uniprot AC)") |
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can we also add single-letter options for these, as there are for the other options?
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| upids =[args.u] if args.u else pd.read_csv(args.i)['Uniprot AC'].dropna().astype(str).tolist() | ||
| if args.u: | ||
| protein_data = [{args.protein_col: args.u, args.uniprot_col: args.u}] |
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can we add an option that allows us to input protein name as well?
so we don't need to use args.u for protein col name
| if proteins_without_cofactors: | ||
| print(f"Proteins without cofactors: {len(proteins_without_cofactors)}") | ||
| print("-"*60) | ||
| print(", ".join(proteins_without_cofactors)) |
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can we have this without space?
",".join(...)
| print("\n" + "="*60) | ||
| if proteins_without_cofactors: | ||
| print(f"Proteins without cofactors: {len(proteins_without_cofactors)}") | ||
| print("-"*60) |
| print(f"Proteins without cofactors: {len(proteins_without_cofactors)}") | ||
| print("-"*60) | ||
| print(", ".join(proteins_without_cofactors)) | ||
| print("-"*60) |
| print("-"*60) | ||
| print(", ".join(proteins_without_cofactors)) | ||
| print("-"*60) | ||
| print("\nThese proteins can be used to run MAVISp.") |
| print("\nThese proteins can be used to run MAVISp.") | ||
| else: | ||
| print("All proteins have cofactors.") | ||
| print("="*60) |
mtiberti
requested changes
Jan 27, 2026
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mtiberti
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mtiberti
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can you please
- update the examples so that they have been run with the latest version
- double check that option
-ais actually used when it supposed to; in my test I obtained asummary_output.csvwith uniprot ID in both column name and protein name while using-a
(python ../../../find_cofactor.py -u P40692 -a MLH1 -p AF_MLH1a_1-341.pdb -s 1 -e 341 -c ../../../cofactors_dict.json -l ions.txt -n A)
added 2 commits
January 27, 2026 12:22
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#12