script to retrieve the UniProt id for a particular PDB id

pdb_rest_example_get_uniprot_for_pdbid.py

#!/usr/bin/env python
# example from https://github.com/PDBeurope/PDBe_Programming/blob/master/REST_API/snippets/basic_get_post.py
# edited to use the python 'requests' module, and to get the UniProt id. for a particular PDBe entry id.

import argparse
import sys
import requests # this is used to access json files

PY3 = sys.version > '3'

if PY3:
    import urllib.request as urllib2
else:
    import urllib2

SERVER_URL = "https://www.ebi.ac.uk/pdbe/api"

UNIPROT = "/mappings/uniprot"

#====================================================================#

def get_request(url, arg, pretty=False):
    full_url = "%s/%s/%s?pretty=%s" % (SERVER_URL, url, arg, str(pretty).lower())
    # e.g. for PDB id. 1ivv we get:
    # full_url = https://www.ebi.ac.uk/pdbe/api//mappings/uniprot/1ivv?pretty=true
    print("This is the url string:\n{}".format(full_url))

    json_results = requests.get( full_url ).json() #This calls the information back from the API using the 'requests' module, and converts it to json format

    # pull out the UniProt id. for this PDB id:
    uniprot_id = json_results[arg] # 'arg' is the input PDB ID e.g. 1ivv
    uniprot_id2 = uniprot_id["UniProt"]
    uniprot_id3 = list(uniprot_id2.keys()) # a list of the UniProt ids. for this input PDB id.
    assert(len(uniprot_id3) == 1)
    uniprot_id4 = uniprot_id3[0]
    print("UniProt id=",uniprot_id4)

    return uniprot_id

#====================================================================#

if __name__ == '__main__':
    parser = argparse.ArgumentParser(formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument('-e', type=str, default=None, action='store', help='the uniprotid')
    args = parser.parse_args()

    # If you type:
    # % python3 pdb_rest_example_get_uniprot_for_pdbid.py
    # You will see:
    #  usage: pdb_rest_example_get_uniprot_for_pdbid.py [-h] [-e E]
    #
 # optional arguments:
    #       -h, --help  show this help message and exit
    #       -e E        the uniprotid

    # Note we defined at the top of the script that:
    # INPDB = "/mappings/uniprot"

    if args.e:
        response = get_request(UNIPROT, args.e, True)
    else:
        parser.print_help()
        sys.exit(1)

    print("FINISHED\n")

#====================================================================#