[BUG] Uniprot annotations not working (mouse genome)

[vphadnis]

Describe the bug
In brieflow analysis jupyter notebook 2.configure_sbs_params, the Uniprot annotations don't seem to work. I suspect this is because I'm working with a mouse cell line, but am not sure.

To Reproduce
In barcode design table standardization block
Matteo should be able to see my jupyter notebook
https://github.com/vphadnis/pilot-screen/blob/main/analysis/2.configure_sbs_params.ipynb

Expected behavior
Expected uniprot_entry column to populate

Screenshots

[mat10d]

Root cause: 2.configure_sbs_params called get_uniprot_data() with no argument, so the annotation download was hardwired to human (NCBI taxon 9606). For a mouse line, none of the mouse gene names match the human UniProt table, so uniprot_entry comes back empty — exactly what you saw.

The underlying get_uniprot_data(species_id=...) already supports other organisms; the notebook just never exposed it.

Fix (PRs):

• brieflow-analysis#74 — adds a SPECIES_ID param to 2.configure_sbs_params and passes it through. For your mouse screen, set:

  SPECIES_ID = "10090"   # Mus musculus

  (human=9606, mouse=10090, rat=10116, fly=7227, worm=6239)
• brieflow#231 — hardens the annotation downloads: adds a User-Agent header (UniProt/STRING/CORUM/MSigDB increasingly reject headerless requests) + an optional cache_path.

Once merged, re-run the barcode-standardization block with SPECIES_ID = "10090" and uniprot_entry should populate for mouse genes. If a few still don't map, it'll be gene-symbol naming differences (mouse Title-case vs UniProt records) rather than the wrong organism.

[mat10d]

Fixed in #231