| Previous changeset 10:8d0c12c9241d (2017-04-09) Next changeset 12:e188a09bf012 (2017-06-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mergegffs commit ad724f17fc3d039b3ca143ab0c025db924c520a1 |
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modified:
mergegffs.py test-data/output.gff |
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| diff -r 8d0c12c9241d -r 791fae70fa3c mergegffs.py --- a/mergegffs.py Sun Apr 09 09:43:42 2017 -0400 +++ b/mergegffs.py Sun Apr 09 10:21:46 2017 -0400 |
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| @@ -25,16 +25,16 @@ db = gffutils.create_db(args.peptides, dbfn=args.database, force=True, keep_order=True,merge_strategy='merge', sort_attribute_values=True) if args.blastp is not None: os.system("convert2gff.py -i "+args.blastp+" -g "+args.peptides+" -p blastp -t protein_match -T -x > blastp.gff") - db=db.update("blastp.gff") + db.update("blastp.gff") if args.signalP is not None: os.system("convert2gff.py -i "+args.signalP+" -g "+args.peptides+" -T -p signalP -t signalpep > signalp.gff") - db=db.update("signalP.gff") + db.update("signalp.gff") if args.tmhmm is not None: os.system("convert2gff.py -i "+args.tmhmm+" -g "+args.peptides+" -T -p tmhmm -t trans_helix > tmhmm.gff") - db=db.update("tmhmm.gff") + db.update("tmhmm.gff") if args.pfam is not None: os.system("pfam2gff.py -i "+args.pfam+" -g "+args.peptides+" -T > PFAM.gff") - db=db.update("PFAM.gff") + db.update("PFAM.gff") with open(args.output, 'w') as fout: for f in db.all_features(): |
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| diff -r 8d0c12c9241d -r 791fae70fa3c test-data/output.gff --- a/test-data/output.gff Sun Apr 09 09:43:42 2017 -0400 +++ b/test-data/output.gff Sun Apr 09 10:21:46 2017 -0400 |
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| b'@@ -47552,3 +47552,38884 @@\n TRINITY_DN9_c0_g1_i1\ttransdecoder\texon\t1\t1138\t.\t+\t.\tID=TRINITY_DN9_c0_g1_i1|m.8905.exon1;Parent=TRINITY_DN9_c0_g1_i1|m.8905\n TRINITY_DN9_c0_g1_i1\ttransdecoder\tCDS\t28\t573\t.\t+\t.\tID=cds.TRINITY_DN9_c0_g1_i1|m.8905;Parent=TRINITY_DN9_c0_g1_i1|m.8905\n TRINITY_DN9_c0_g1_i1\ttransdecoder\tthree_prime_UTR\t574\t1138\t.\t+\t.\tID=TRINITY_DN9_c0_g1_i1|m.8905.utr3p1;Parent=TRINITY_DN9_c0_g1_i1|m.8905\n+TRINITY_DN1000_c0_g1_i1\tblastp\tprotein_match\t1606\t1496\t0\t-\t.\tID=TRINITY_DN1000_c0_g1_i1|m.4108.protein_match;query=TRINITY_DN1000_c0_g1_i1|m.4108\n+TRINITY_DN1000_c0_g1_i1\tblastp\tprotein_match\t1138\t837\t0\t+\t.\tID=TRINITY_DN1000_c0_g1_i1|m.4107.protein_match;query=TRINITY_DN1000_c0_g1_i1|m.4107\n+TRINITY_DN1002_c0_g1_i1\tblastp\tprotein_match\t3539\t2359\t0\t+\t.\tID=TRINITY_DN1002_c0_g1_i1|m.4087.protein_match;query=TRINITY_DN1002_c0_g1_i1|m.4087\n+TRINITY_DN1002_c0_g2_i1\tblastp\tprotein_match\t3540\t3209\t0\t+\t.\tID=TRINITY_DN1002_c0_g2_i1|m.4089.protein_match;query=TRINITY_DN1002_c0_g2_i1|m.4089\n+TRINITY_DN1002_c0_g2_i1\tblastp\tprotein_match\t2294\t1529\t0\t+\t.\tID=TRINITY_DN1002_c0_g2_i1|m.4088.protein_match;query=TRINITY_DN1002_c0_g2_i1|m.4088\n+TRINITY_DN1003_c0_g1_i1\tblastp\tprotein_match\t2048\t1534\t0\t+\t.\tID=TRINITY_DN1003_c0_g1_i1|m.4132.protein_match;query=TRINITY_DN1003_c0_g1_i1|m.4132\n+TRINITY_DN1003_c0_g1_i1\tblastp\tprotein_match\t2649\t2457\t0\t+\t.\tID=TRINITY_DN1003_c0_g1_i1|m.4133.protein_match;query=TRINITY_DN1003_c0_g1_i1|m.4133\n+TRINITY_DN1003_c0_g2_i1\tblastp\tprotein_match\t2648\t1933\t0\t+\t.\tID=TRINITY_DN1003_c0_g2_i1|m.4134.protein_match;query=TRINITY_DN1003_c0_g2_i1|m.4134\n+TRINITY_DN1004_c0_g1_i1\tblastp\tprotein_match\t1978\t1809\t0\t-\t.\tID=TRINITY_DN1004_c0_g1_i1|m.4152.protein_match;query=TRINITY_DN1004_c0_g1_i1|m.4152\n+TRINITY_DN1004_c0_g1_i1\tblastp\tprotein_match\t1738\t1180\t0\t+\t.\tID=TRINITY_DN1004_c0_g1_i1|m.4151.protein_match;query=TRINITY_DN1004_c0_g1_i1|m.4151\n+TRINITY_DN1006_c0_g1_i1\tblastp\tprotein_match\t1690\t1322\t0\t+\t.\tID=TRINITY_DN1006_c0_g1_i1|m.4045.protein_match;query=TRINITY_DN1006_c0_g1_i1|m.4045\n+TRINITY_DN1007_c0_g1_i1\tblastp\tprotein_match\t1712\t1202\t0\t+\t.\tID=TRINITY_DN1007_c0_g1_i1|m.4176.protein_match;query=TRINITY_DN1007_c0_g1_i1|m.4176\n+TRINITY_DN1008_c0_g1_i1\tblastp\tprotein_match\t2777\t1988\t0\t+\t.\tID=TRINITY_DN1008_c0_g1_i1|m.4183.protein_match;query=TRINITY_DN1008_c0_g1_i1|m.4183\n+TRINITY_DN1009_c0_g1_i1\tblastp\tprotein_match\t929\t619\t0\t+\t.\tID=TRINITY_DN1009_c0_g1_i1|m.4109.protein_match;query=TRINITY_DN1009_c0_g1_i1|m.4109\n+TRINITY_DN1009_c0_g2_i1\tblastp\tprotein_match\t1174\t782\t0\t+\t.\tID=TRINITY_DN1009_c0_g2_i1|m.4110.protein_match;query=TRINITY_DN1009_c0_g2_i1|m.4110\n+TRINITY_DN100_c0_g1_i1\tblastp\tprotein_match\t2157\t1501\t0\t+\t.\tID=TRINITY_DN100_c0_g1_i1|m.43.protein_match;query=TRINITY_DN100_c0_g1_i1|m.43\n+TRINITY_DN1010_c0_g1_i1\tblastp\tprotein_match\t1762\t1589\t1\t-\t.\tID=TRINITY_DN1010_c0_g1_i1|m.4178.protein_match;query=TRINITY_DN1010_c0_g1_i1|m.4178\n+TRINITY_DN1010_c0_g1_i1\tblastp\tprotein_match\t964\t717\t0\t-\t.\tID=TRINITY_DN1010_c0_g1_i1|m.4177.protein_match;query=TRINITY_DN1010_c0_g1_i1|m.4177\n+TRINITY_DN1010_c0_g2_i1\tblastp\tprotein_match\t458\t347\t0\t+\t.\tID=TRINITY_DN1010_c0_g2_i1|m.4181.protein_match;query=TRINITY_DN1010_c0_g2_i1|m.4181\n+TRINITY_DN1010_c0_g2_i1\tblastp\tprotein_match\t1820\t1647\t1\t-\t.\tID=TRINITY_DN1010_c0_g2_i1|m.4180.protein_match;query=TRINITY_DN1010_c0_g2_i1|m.4180\n+TRINITY_DN1010_c0_g2_i1\tblastp\tprotein_match\t1022\t775\t0\t-\t.\tID=TRINITY_DN1010_c0_g2_i1|m.4179.protein_match;query=TRINITY_DN1010_c0_g2_i1|m.4179\n+TRINITY_DN1011_c0_g1_i1\tblastp\tprotein_match\t864\t599\t0\t+\t.\tID=TRINITY_DN1011_c0_g1_i1|m.4092.protein_match;query=TRINITY_DN1011_c0_g1_i1|m.4092\n+TRINITY_DN1011_c0_g2_i1\tblastp\tprotein_match\t1185\t813\t0\t+\t.\tID=TRINITY_DN1011_c0_g2_i1|m.4093.protein_match;query=TRINITY_DN1011_c0_g2_i1|m.4093\n+TRINITY_DN1012_c0_g1_i1\tblastp\tprotein_match\t1587\t1197\t0\t+\t.\tID=TRINITY_DN1012_c0_g1_i1|m.4159.protein_match;query=TRINITY_DN1012_c0_g1_i1|m.4159\n+TRINITY_DN1012_c0_g2_i1\tblastp\tprotein_match\t1849\t1459\t0\t+\t.\tID=TRINITY_DN1'..b'1_i1\thmmscan\tPFAM\t661\t706\t16.5\t+\t.\tID=TRINITY_DN996_c0_g1_i1|m.998.Acetyltransf_10.1;Name=PF13673.Acetyltransf_10.1\n+TRINITY_DN996_c0_g1_i1\thmmscan\tPFAM\t463\t550\t14.4\t+\t.\tID=TRINITY_DN996_c0_g1_i1|m.998.MOZ_SAS.1;Name=PF01853.MOZ_SAS.1\n+TRINITY_DN996_c0_g1_i1\thmmscan\tPFAM\t658\t682\t13.3\t+\t.\tID=TRINITY_DN996_c0_g1_i1|m.998.Acetyltransf_7.1;Name=PF13508.Acetyltransf_7.1\n+TRINITY_DN996_c0_g2_i1\thmmscan\tPFAM\t88\t230\t88.6\t+\t.\tID=TRINITY_DN996_c0_g2_i1|m.999.Hat1_N.1;Name=PF10394.Hat1_N.1\n+TRINITY_DN996_c0_g2_i1\thmmscan\tPFAM\t583\t640\t17.1\t+\t.\tID=TRINITY_DN996_c0_g2_i1|m.999.Acetyltransf_1.1;Name=PF00583.Acetyltransf_1.1\n+TRINITY_DN996_c0_g2_i1\thmmscan\tPFAM\t661\t706\t16.3\t+\t.\tID=TRINITY_DN996_c0_g2_i1|m.999.Acetyltransf_10.1;Name=PF13673.Acetyltransf_10.1\n+TRINITY_DN996_c0_g2_i1\thmmscan\tPFAM\t463\t549\t14.1\t+\t.\tID=TRINITY_DN996_c0_g2_i1|m.999.MOZ_SAS.1;Name=PF01853.MOZ_SAS.1\n+TRINITY_DN996_c0_g2_i1\thmmscan\tPFAM\t658\t682\t13.1\t+\t.\tID=TRINITY_DN996_c0_g2_i1|m.999.Acetyltransf_7.1;Name=PF13508.Acetyltransf_7.1\n+TRINITY_DN997_c0_g2_i1\thmmscan\tPFAM\t650\t732\t68.8\t+\t.\tID=TRINITY_DN997_c0_g2_i1|m.996.ARID.1;Name=PF01388.ARID.1\n+TRINITY_DN998_c0_g1_i1\thmmscan\tPFAM\t275\t606\t262.9\t+\t.\tID=TRINITY_DN998_c0_g1_i1|m.1034.Oxysterol_BP.1;Name=PF01237.Oxysterol_BP.1\n+TRINITY_DN998_c0_g2_i1\thmmscan\tPFAM\t172\t503\t263.0\t+\t.\tID=TRINITY_DN998_c0_g2_i1|m.1035.Oxysterol_BP.1;Name=PF01237.Oxysterol_BP.1\n+TRINITY_DN999_c0_g1_i1\thmmscan\tPFAM\t131\t426\t330.1\t+\t.\tID=TRINITY_DN999_c0_g1_i1|m.976.Lyase_1.1;Name=PF00206.Lyase_1.1\n+TRINITY_DN999_c0_g1_i1\thmmscan\tPFAM\t1205\t1272\t82.4\t+\t.\tID=TRINITY_DN999_c0_g1_i1|m.976.ASL_C2.1;Name=PF14698.ASL_C2.1\n+TRINITY_DN999_c0_g2_i1\thmmscan\tPFAM\t131\t409\t301.5\t+\t.\tID=TRINITY_DN999_c0_g2_i1|m.977.Lyase_1.1;Name=PF00206.Lyase_1.1\n+TRINITY_DN999_c0_g2_i1\thmmscan\tPFAM\t1206\t1273\t84.6\t+\t.\tID=TRINITY_DN999_c0_g2_i1|m.978.ASL_C2.1;Name=PF14698.ASL_C2.1\n+TRINITY_DN99_c0_g1_i1\thmmscan\tPFAM\t221\t715\t688.5\t+\t.\tID=TRINITY_DN99_c0_g1_i1|m.8865.Rad17.1;Name=PF03215.Rad17.1\n+TRINITY_DN99_c0_g1_i1\thmmscan\tPFAM\t347\t479\t29.2\t+\t.\tID=TRINITY_DN99_c0_g1_i1|m.8865.AAA_22.1;Name=PF13401.AAA_22.1\n+TRINITY_DN99_c0_g1_i1\thmmscan\tPFAM\t353\t451\t27.2\t+\t.\tID=TRINITY_DN99_c0_g1_i1|m.8865.AAA.1;Name=PF00004.AAA.1\n+TRINITY_DN99_c0_g1_i1\thmmscan\tPFAM\t347\t455\t24.8\t+\t.\tID=TRINITY_DN99_c0_g1_i1|m.8865.AAA_14.1;Name=PF13173.AAA_14.1\n+TRINITY_DN99_c0_g1_i1\thmmscan\tPFAM\t356\t402\t21.2\t+\t.\tID=TRINITY_DN99_c0_g1_i1|m.8865.AAA_18.2;Name=PF13238.AAA_18.2\n+TRINITY_DN99_c0_g1_i1\thmmscan\tPFAM\t356\t392\t18.8\t+\t.\tID=TRINITY_DN99_c0_g1_i1|m.8865.RNA_helicase.1;Name=PF00910.RNA_helicase.1\n+TRINITY_DN99_c0_g1_i1\thmmscan\tPFAM\t353\t459\t15.6\t+\t.\tID=TRINITY_DN99_c0_g1_i1|m.8865.Mg_chelatase.1;Name=PF01078.Mg_chelatase.1\n+TRINITY_DN99_c0_g1_i1\thmmscan\tPFAM\t938\t970\t12.4\t+\t.\tID=TRINITY_DN99_c0_g1_i1|m.8865.AAA_assoc_2.1;Name=PF16193.AAA_assoc_2.1\n+TRINITY_DN99_c0_g1_i1\thmmscan\tPFAM\t329\t357\t12.0\t+\t.\tID=TRINITY_DN99_c0_g1_i1|m.8865.AAA_19.1;Name=PF13245.AAA_19.1\n+TRINITY_DN99_c0_g2_i1\thmmscan\tPFAM\t221\t715\t688.4\t+\t.\tID=TRINITY_DN99_c0_g2_i1|m.8866.Rad17.1;Name=PF03215.Rad17.1\n+TRINITY_DN99_c0_g2_i1\thmmscan\tPFAM\t347\t479\t29.2\t+\t.\tID=TRINITY_DN99_c0_g2_i1|m.8866.AAA_22.1;Name=PF13401.AAA_22.1\n+TRINITY_DN99_c0_g2_i1\thmmscan\tPFAM\t353\t451\t27.1\t+\t.\tID=TRINITY_DN99_c0_g2_i1|m.8866.AAA.1;Name=PF00004.AAA.1\n+TRINITY_DN99_c0_g2_i1\thmmscan\tPFAM\t347\t455\t24.7\t+\t.\tID=TRINITY_DN99_c0_g2_i1|m.8866.AAA_14.1;Name=PF13173.AAA_14.1\n+TRINITY_DN99_c0_g2_i1\thmmscan\tPFAM\t356\t402\t21.1\t+\t.\tID=TRINITY_DN99_c0_g2_i1|m.8866.AAA_18.2;Name=PF13238.AAA_18.2\n+TRINITY_DN99_c0_g2_i1\thmmscan\tPFAM\t356\t392\t18.7\t+\t.\tID=TRINITY_DN99_c0_g2_i1|m.8866.RNA_helicase.1;Name=PF00910.RNA_helicase.1\n+TRINITY_DN99_c0_g2_i1\thmmscan\tPFAM\t353\t459\t15.5\t+\t.\tID=TRINITY_DN99_c0_g2_i1|m.8866.Mg_chelatase.1;Name=PF01078.Mg_chelatase.1\n+TRINITY_DN99_c0_g2_i1\thmmscan\tPFAM\t938\t970\t12.4\t+\t.\tID=TRINITY_DN99_c0_g2_i1|m.8866.AAA_assoc_2.1;Name=PF16193.AAA_assoc_2.1\n+TRINITY_DN99_c0_g2_i1\thmmscan\tPFAM\t329\t357\t12.0\t+\t.\tID=TRINITY_DN99_c0_g2_i1|m.8866.AAA_19.1;Name=PF13245.AAA_19.1\n' 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