Get a protein sequence from UniProt when you only have that protein's name, not its accession. Uses http://gist.github.com/329730.

get_sequence_from_name.py

import uniprot_mapping
import urllib2

def main(file):
    fh = open(file, 'r')
    for line in fh.readlines():
        if not line.startswith('"'): #ignore comment lines
            name = line.rstrip()
            id = uniprot_mapping.uniprot_mapping('ACC+ID', 'ACC', name)
            mapped = parse_return_string(id)
            if not mapped[1]:
                print(name) #something went wrong
            else:
                seq_url = 'http://www.uniprot.org/uniprot/'+mapped[1]+'.fasta'
                response = urllib2.urlopen(seq_url)
                out = open('seqs/'+mapped[1]+'.fa', 'w')
                out.write(response.read())
                out.close()

def parse_return_string(string):
    from_id = None
    to_id = None
    lines = string.split('\n') #removes first element from list, always header
    lines.pop(0)
    for line in lines:
        if not to_id: #only get the first id - single accession sufficient
            try:
                from_id = line.split('\t')[0]
                to_id = line.split('\t')[1]
            except IndexError: #nothing in the list :(
                print 'ERROR:'
                print string
    return (from_id, to_id)

if __name__ == '__main__':
    main('./proteins') #assumes list of names in this file

gistfile2.txt