Mercurial > repos > jjjjia > cpo_prediction

comparison cpo_galaxy_prediction.py @ 6:cabceaa239e4 draft

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planemo upload
author jjjjia
date Thu, 23 Aug 2018 12:21:15 -0400
parents 698579246d0d
children a14b12a71a53
comparison
equal deleted inserted replaced
5:698579246d0d 6:cabceaa239e4
24 import collections 24 import collections
25 import json 25 import json
26 import numpy 26 import numpy
27 27
28 28
29 debug = True #debug skips the shell scripts and also dump out a ton of debugging messages 29 debug = False #debug skips the shell scripts and also dump out a ton of debugging messages
30 30
31 if not debug: 31 if not debug:
32 #parses some parameters 32 #parses some parameters
33 parser = optparse.OptionParser("Usage: %prog [options] arg1 arg2 ...") 33 parser = optparse.OptionParser("Usage: %prog [options] arg1 arg2 ...")
34 #required 34 #required
594 for item in output: 594 for item in output:
595 out.write("%s\n" % item) 595 out.write("%s\n" % item)
596 596
597 597
598 #TSV output 598 #TSV output
599 lindaOut = []
599 tsvOut = [] 600 tsvOut = []
600 tsvOut.append("ID\tExpected Species\tMLST Species\tSequence Type\tMLST Scheme\tCarbapenem Resistance Genes\tOther AMR Genes\tTotal Plasmids\tPlasmids ID\tNum_Contigs\tPlasmid Length\tPlasmid RepType\tPlasmid Mobility\tNearest Reference\tDefinitely Plasmid Contigs\tLikely Plasmid Contigs") 601 lindaOut.append("new\tID\tQUALITY\tExpected Species\tMLST Scheme\tSequence Type\tMLST_ALLELE_1\tMLST_ALLELE_2\tMLST_ALLELE_3\tMLST_ALLELE_4\tMLST_ALLELE_5\tMLST_ALLELE_6\tMLST_ALLELE_7\tSEROTYPE\tK_CAPSULE\tPLASMID_1_FAMILY\tPLASMID_1_BEST_MATCH\tPLASMID_1_COVERAGE\tPLASMID_1_SNVS_TO_BEST_MATCH\tPLASMID_1_CARBAPENEMASE\tPLASMID_1_INC_GROUP\tPLASMID_2_RFLP\tPLASMID_2_FAMILY\tPLASMID_2_BEST_MATCH\tPLASMID_2_COVERAGE\tPLASMID_2_SNVS_TO_BEST_MATCH\tPLASMID_2_CARBAPENEMASE\tPLASMID_2_INC_GROUP")
602
603 tsvOut.append("new\tID\tExpected Species\tMLST Species\tSequence Type\tMLST Scheme\tCarbapenem Resistance Genes\tOther AMR Genes\tTotal Plasmids\tPlasmids ID\tNum_Contigs\tPlasmid Length\tPlasmid RepType\tPlasmid Mobility\tNearest Reference\tDefinitely Plasmid Contigs\tLikely Plasmid Contigs")
601 #start with ID 604 #start with ID
602 temp = "" 605 temp = "\t"
603 temp += (ID + "\t") 606 temp += (ID + "\t")
604 temp += expectedSpecies + "\t" 607 temp += expectedSpecies + "\t"
605 608
606 #move into MLST 609 #move into MLST
607 temp += mlstHit.species + "\t" 610 temp += mlstHit.species + "\t"