diff mergegffs.py @ 0:2b2efd0c4df8 draft

planemo upload commit 7bc2a91afe5fcf29893e582382aa874eacb1c1ca

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergegffs.py	Fri Apr 07 17:27:31 2017 -0400
@@ -0,0 +1,42 @@
+import sys
+import os
+import gffutils
+import argparse
+
+
+
+
+def main(argv, wayout):
+        if not len(argv):
+                argv.append("-h")
+        parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=__doc__)
+        parser.add_argument('-m','--genemap', help="mapping of genes to transcripts")
+        parser.add_argument('-p','--peptides',required=True, help="peptide prediction gff")
+        parser.add_argument('-b','--blastp', help="blastp outfmt6 results for peptides")
+        parser.add_argument('-f','--pfam', help="hmmer results for peptides")
+        parser.add_argument('-t','--tmhmm', help="tmhmm results for peptides")
+        parser.add_argument('-s','--signalP', help="signalP results for peptides")
+        parser.add_argument('-d','--database', required=True, help="gff database to load or create")
+        parser.add_argument('-o','--output', required=True, help="output in gff format")
+        args = parser.parse_args(argv)
+
+
+        db = gffutils.create_db(args.peptides, dbfn=args.database, force=True, keep_order=True,merge_strategy='merge', sort_attribute_values=True)
+        if args.blastp == True:
+            os.system("blast2genomegff.py -b "+args.blastp+" -g  -d "+args.peptides+" -p blastp -t protein_match -T  -x > blastp.gff")
+            db=db.update(args.blastp)
+        if args.blastp == True:
+            os.system("convert2gff.py -i "+args.signalP+" -g "+args.peptides+" -T -t signalP > signalp.gff")
+            db=db.update(args.blastp)
+        if args.blastp == True:
+            os.system("convert2gff.py -i "+args.tmhmm+" -g "+args.peptides+" -T -t tmhmm > tmhmm.gff")
+            db=db.update(args.blastp)
+        if args.blastp == True:
+            os.system("pfam2gff.py -i "+args.pfam+" -g "+args.peptides+" -T > PFAM.gff")
+            db=db.update(args.blastp)
+
+        with open(args.output, 'w') as fout:
+            for f in db.all_features():
+                fout.write(str(f) + '\n')
+if __name__ == "__main__":
+        main(sys.argv[1:],sys.stdout)