protein-quest

Python package to search/retrieve/filter proteins and protein structures.

It uses

• Uniprot Sparql endpoint to search for proteins and their measured or predicted 3D structures.
• Uniprot taxonomy to search for taxonomy.
• QuickGO to search for Gene Ontology terms.
• gemmi to work with macromolecular models.
• dask-distributed to compute in parallel.

An example command:

protein-quest search uniprot \
    --taxon-id 9606 \
    --reviewed \
    --subcellular-location-uniprot nucleus \
    --subcellular-location-go GO:0005634 \
    --molecular-function-go GO:0003677 \
    --limit 100 \
    uniprot_accs.txt