Unclear fasta spec

[jkosinski]

AlphaPulldown/README.md

Line 52 in 8b465a3

- **FASTA file paths** instead of UniProt IDs: `/path/to/protein.fasta`

It is a bit unclear whether the fasta file can have multiple proteins/sequences or it should be one fasta per protein. I don't know and could you rephrase to make it clearer (but still concise)?

Related to that, if multi-protein fasta is not supported yet by the snakemake pipeline, this should be reported as an issue to fix.

[DimaMolod]

No, fasta files with multiple entries can't be used with snakemake by definition (1 file - 1 job). For that exact reason @maurerv added s splitter script to the repo:
https://github.com/KosinskiLab/AlphaPulldownSnakemake/blob/main/config/split_fasta.py