Mercurial > repos > eduardo > mergegffs

comparison mergegffs.py @ 10:8d0c12c9241d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mergegffs commit c9b4085466b82054831df7bb14a8ebe1fdc3e164-dirty
author eduardo
date Sun, 09 Apr 2017 09:43:42 -0400
parents 79d6bb2e6a5d
children 791fae70fa3c
comparison
equal deleted inserted replaced
9:79d6bb2e6a5d 10:8d0c12c9241d
21 parser.add_argument('-o','--output', required=True, help="output in gff format") 21 parser.add_argument('-o','--output', required=True, help="output in gff format")
22 args = parser.parse_args(argv) 22 args = parser.parse_args(argv)
23 23
24 24
25 db = gffutils.create_db(args.peptides, dbfn=args.database, force=True, keep_order=True,merge_strategy='merge', sort_attribute_values=True) 25 db = gffutils.create_db(args.peptides, dbfn=args.database, force=True, keep_order=True,merge_strategy='merge', sort_attribute_values=True)
26 if args.blastp == True: 26 if args.blastp is not None:
27 os.system("blast2genomegff.py -b "+args.blastp+" -g -d "+args.peptides+" -p blastp -t protein_match -T -x > blastp.gff") 27 os.system("convert2gff.py -i "+args.blastp+" -g "+args.peptides+" -p blastp -t protein_match -T -x > blastp.gff")
28 db=db.update(args.blastp) 28 db=db.update("blastp.gff")
29 if args.blastp == True: 29 if args.signalP is not None:
30 os.system("convert2gff.py -i "+args.signalP+" -g "+args.peptides+" -T -t signalP > signalp.gff") 30 os.system("convert2gff.py -i "+args.signalP+" -g "+args.peptides+" -T -p signalP -t signalpep > signalp.gff")
31 db=db.update(args.blastp) 31 db=db.update("signalP.gff")
32 if args.blastp == True: 32 if args.tmhmm is not None:
33 os.system("convert2gff.py -i "+args.tmhmm+" -g "+args.peptides+" -T -t tmhmm > tmhmm.gff") 33 os.system("convert2gff.py -i "+args.tmhmm+" -g "+args.peptides+" -T -p tmhmm -t trans_helix > tmhmm.gff")
34 db=db.update(args.blastp) 34 db=db.update("tmhmm.gff")
35 if args.blastp == True: 35 if args.pfam is not None:
36 os.system("pfam2gff.py -i "+args.pfam+" -g "+args.peptides+" -T > PFAM.gff") 36 os.system("pfam2gff.py -i "+args.pfam+" -g "+args.peptides+" -T > PFAM.gff")
37 db=db.update(args.blastp) 37 db=db.update("PFAM.gff")
38 38
39 with open(args.output, 'w') as fout: 39 with open(args.output, 'w') as fout:
40 for f in db.all_features(): 40 for f in db.all_features():
41 fout.write(str(f) + '\n') 41 fout.write(str(f) + '\n')
42 if __name__ == "__main__": 42 if __name__ == "__main__":