comparison cpo_galaxy_prediction.py @ 6:cabceaa239e4 draft

planemo upload

5:698579246d0d

import collections
import json
import numpy


debug = True #debug skips the shell scripts and also dump out a ton of debugging messages

if not debug:
    #parses some parameters
    parser = optparse.OptionParser("Usage: %prog [options] arg1 arg2 ...")
    #required

    for item in output:
        out.write("%s\n" % item)


    #TSV output
    tsvOut = []
    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")
    #start with ID
    temp = ""
    temp += (ID + "\t")
    temp += expectedSpecies + "\t"

    #move into MLST
    temp += mlstHit.species + "\t"

6:cabceaa239e4

import collections
import json
import numpy


debug = False #debug skips the shell scripts and also dump out a ton of debugging messages

if not debug:
    #parses some parameters
    parser = optparse.OptionParser("Usage: %prog [options] arg1 arg2 ...")
    #required

    for item in output:
        out.write("%s\n" % item)


    #TSV output
    lindaOut = []
    tsvOut = []
    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")

    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")
    #start with ID
    temp = "\t"
    temp += (ID + "\t")
    temp += expectedSpecies + "\t"

    #move into MLST
    temp += mlstHit.species + "\t"