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annotate 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
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1 import sys
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2 import os
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3 import gffutils
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4 import argparse
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9 def main(argv, wayout):
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10 if not len(argv):
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11 argv.append("-h")
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12 parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=__doc__)
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13 parser.add_argument('-m','--genemap', help="mapping of genes to transcripts")
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14 parser.add_argument('-p','--peptides',required=True, help="peptide prediction gff")
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15 parser.add_argument('-b','--blastp', help="blastp outfmt6 results for peptides")
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16 parser.add_argument('-x','--blastx', help="blastx outfmt6 results for transcripts")
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17 parser.add_argument('-f','--pfam', help="hmmer results for peptides")
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18 parser.add_argument('-t','--tmhmm', help="tmhmm results for peptides")
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19 parser.add_argument('-s','--signalP', help="signalP results for peptides")
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20 parser.add_argument('-d','--database', required=True, help="gff database to load or create")
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21 parser.add_argument('-o','--output', required=True, help="output in gff format")
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22 args = parser.parse_args(argv)
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25 db = gffutils.create_db(args.peptides, dbfn=args.database, force=True, keep_order=True,merge_strategy='merge', sort_attribute_values=True)
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26 if args.blastp is not None:
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27 os.system("convert2gff.py -i "+args.blastp+" -g "+args.peptides+" -p blastp -t protein_match -T -x > blastp.gff")
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28 db=db.update("blastp.gff")
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29 if args.signalP is not None:
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30 os.system("convert2gff.py -i "+args.signalP+" -g "+args.peptides+" -T -p signalP -t signalpep > signalp.gff")
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31 db=db.update("signalp.gff")
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32 if args.tmhmm is not None:
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33 os.system("convert2gff.py -i "+args.tmhmm+" -g "+args.peptides+" -T -p tmhmm -t trans_helix > tmhmm.gff")
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34 db=db.update("tmhmm.gff")
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35 if args.pfam is not None:
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36 os.system("pfam2gff.py -i "+args.pfam+" -g "+args.peptides+" -T > PFAM.gff")
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37 db=db.update("PFAM.gff")
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39 with open(args.output, 'w') as fout:
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40 for f in db.all_features():
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41 fout.write(str(f) + '\n')
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42 if __name__ == "__main__":
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43 main(sys.argv[1:],sys.stdout)