Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_galaxy_prediction.py @ 24:e5a7da2239af draft

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planemo upload
author jjjjia
date Wed, 29 Aug 2018 02:31:49 -0400
parents 2cca036ceb91
children 573136f142b6
comparison
equal deleted inserted replaced
23:2cca036ceb91 24:e5a7da2239af
675 lindaOut.append(lindaTemp) 675 lindaOut.append(lindaTemp)
676 out = open("summary.linda.tsv", 'w') 676 out = open("summary.linda.tsv", 'w')
677 for item in lindaOut: 677 for item in lindaOut:
678 out.write("%s\n" % item) 678 out.write("%s\n" % item)
679 679
680 tsvOut.append("new\tID\tExpected Species\tMLST Species\tSequence Type\tMLST Scheme\tCarbapenem Resistance Genes\tOther AMR Genes\tPlasmid Best Match\tTotal Plasmids\tPlasmids ID\tNum_Contigs\tPlasmid Length\tPlasmid RepType\tPlasmid Mobility\tNearest Reference\tDefinitely Plasmid Contigs\tLikely Plasmid Contigs") 680 tsvOut.append("new\tID\tExpected Species\tMLST Species\tSequence Type\tMLST Scheme\tCarbapenem Resistance Genes\tOther AMR Genes\tPlasmid Best Match\tPlasmid Identity\tPlasmid Shared Hash\tTotal Plasmids\tPlasmids ID\tNum_Contigs\tPlasmid Length\tPlasmid RepType\tPlasmid Mobility\tNearest Reference\tDefinitely Plasmid Contigs\tLikely Plasmid Contigs")
681 #start with ID 681 #start with ID
682 temp = "\t" 682 temp = "\t"
683 temp += (ID + "\t") 683 temp += (ID + "\t")
684 temp += expectedSpecies + "\t" 684 temp += expectedSpecies + "\t"
685 685
692 temp += ";".join(carbapenamases) + "\t" 692 temp += ";".join(carbapenamases) + "\t"
693 temp += ";".join(amrGenes) + "\t" 693 temp += ";".join(amrGenes) + "\t"
694 694
695 #lastly plasmids 695 #lastly plasmids
696 temp += str(plasmidFamily[list(plasmidFamily.keys())[0]].name) + "\t" 696 temp += str(plasmidFamily[list(plasmidFamily.keys())[0]].name) + "\t"
697 temp += str(plasmidFamily[list(plasmidFamily.keys())[0]].identity) + "\t"
698 temp += str(plasmidFamily[list(plasmidFamily.keys())[0]].sharedHashes) + "\t"
697 temp+= str(len(mSuitePlasmids)) + "\t" 699 temp+= str(len(mSuitePlasmids)) + "\t"
698 plasmidID = "" 700 plasmidID = ""
699 contigs = "" 701 contigs = ""
700 lengths = "" 702 lengths = ""
701 rep_type = "" 703 rep_type = ""