Getting Started

Most examples will be provided as stand-alone runnable code, but some simple examples are included here too.

The following code would print the set of proteins that have a domain at their immediate N termini.

from shephard.apis import uniprot
from shephard.interfaces import si_domains, si_sites

# read in a UniProt based FASTA file
P = uniprot.uniprot_fasta_to_proteome('fasta_file.fasta')

si_domains.add_domains_from_file(P, 'domains_file.tsv')

for protein in P:
    for domain_idx in
        domain = protein.domain(domain_idx)
        if domain.start ==  1:
            print(f'Protein {protein} has an N-terminal domain: {domain}')