Armory_002_DBPR.py

#!/usr/bin/env python
'''
A solution to a ROSALIND bioinformatics problem from the Armory problem area, 
which focuses on using prebuilt bioinformatics packages, in this case BioPython.

Problem Title: Introduction to Protein Databases
Rosalind Armory ID: DBPR
Rosalind Armory #: 002
URL: http://rosalind.info/problems/dbpr/
'''

from Bio import ExPASy
from Bio import SwissProt

with open('data/armory/rosalind_dbpr.txt') as input_data:
	UniProt_ID = input_data.read().strip()

handle = ExPASy.get_sprot_raw(UniProt_ID)
record = SwissProt.read(handle)

bio_proc = []
for item in record.cross_references:
    if item[0] == 'GO' and item[2][0]=='P':
        bio_proc.append(item[2].lstrip('P:'))

print '\n'.join(bio_proc)
with open('output/armory/Armory_002_DBPR.txt', 'w') as output_data:
	output_data.write('\n'.join(bio_proc))