filter obsolete go terms

filter_obs.py

#!/usr/bin/env python

import re
import json
import clint

def import_go(gofile='go.json'):
    try:
        return json.loads(json.load(open(gofile)))
    except IOError:
        goterms = []
        obo = open('gene_ontology_ext.obo').read()
        for chunk in obo.split('[Term]'):
            lines = chunk.splitlines()
            gid = lines[1].replace('id: ','')
            if 'is_obsolete: true' in lines:
                goterms.append(gid)
        return goterms


def main():
    inp = clint.piped_in().splitlines()
    if not inp:
        inp = open(clint.args.get(0)).readlines()
    goterms = import_go()
    filtered = []
    for line in inp:
        goid = line.split('\t')[4]
        if goid in goterms: 
            print line.strip('\n')

if __name__ == '__main__':
    main()