Mercurial > repos > eduardo > mergegffs

comparison mergegffs.py @ 13:742d726397b3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mergegffs commit 230f5fe14cc469e56626201a5c377686976d81fc-dirty
author eduardo
date Mon, 26 Jun 2017 02:56:32 -0400
parents e188a09bf012
children 5e27f44500d6
comparison
equal deleted inserted replaced
12:e188a09bf012 13:742d726397b3
26 if args.blastp is not None: 26 if args.blastp is not None:
27 os.system("convert2gff.py -i "+args.blastp+" -g "+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("blastp.gff") 28 db=db.update("blastp.gff")
29 if args.signalP is not None: 29 if args.signalP is not None:
30 os.system("convert2gff.py -i "+args.signalP+" -g "+args.peptides+" -T -p signalP -t signalpep > signalp.gff") 30 os.system("convert2gff.py -i "+args.signalP+" -g "+args.peptides+" -T -p signalP -t signalpep > signalp.gff")
31 db=db.update("signalP.gff") 31 db=db.update("signalp.gff")
32 if args.tmhmm is not None: 32 if args.tmhmm is not None:
33 os.system("convert2gff.py -i "+args.tmhmm+" -g "+args.peptides+" -T -p tmhmm -t trans_helix > 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("tmhmm.gff") 34 db=db.update("tmhmm.gff")
35 if args.pfam is not None: 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")