Example of Uniprot REST API (Python)

uniprot_rest_example.py

#!/usr/bin/env python

"""
Queries Uniprot database and retrieves (canonical) sequences.
"""

import argparse
import sys
import urllib.request

ap = argparse.ArgumentParser()
ap.add_argument('seqfile', help='Input file with protein names')
ap.add_argument('-o', dest='output', help='Output file for protein sequences')
args = ap.parse_args()

if args.output:
    ostream = open(args.output, 'w')
else:
    ostream = sys.stdout

with open(args.seqfile) as handle:
    for line in handle:
        line = line.strip()
        if not line:
            continue

        url = f'https://www.uniprot.org/uniprot/?query={line}&format=fasta'
        with urllib.request.urlopen(url) as r:
            fasta = r.read().decode('utf-8').strip()
        print(fasta, file=ostream)

if args.output:
    ostream.close()

how make search bases into organism name and perform download the complete proteome?

Could you suggest how to use your snippet to get other information associated with Uniprot entry such as PDB ID, GO, PFAM ID etc?

Thanks very much.