Mercurial > repos > jjjjia > cpo_prediction
diff cpo_galaxy_prediction.py @ 24:e5a7da2239af draft
planemo upload
| author | jjjjia |
|---|---|
| date | Wed, 29 Aug 2018 02:31:49 -0400 |
| parents | 2cca036ceb91 |
| children | 573136f142b6 |
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--- a/cpo_galaxy_prediction.py Wed Aug 29 01:42:01 2018 -0400 +++ b/cpo_galaxy_prediction.py Wed Aug 29 02:31:49 2018 -0400 @@ -677,7 +677,7 @@ for item in lindaOut: out.write("%s\n" % item) - 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") + 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") #start with ID temp = "\t" temp += (ID + "\t") @@ -694,6 +694,8 @@ #lastly plasmids temp += str(plasmidFamily[list(plasmidFamily.keys())[0]].name) + "\t" + temp += str(plasmidFamily[list(plasmidFamily.keys())[0]].identity) + "\t" + temp += str(plasmidFamily[list(plasmidFamily.keys())[0]].sharedHashes) + "\t" temp+= str(len(mSuitePlasmids)) + "\t" plasmidID = "" contigs = ""