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1 #!/home/jjjjia/.conda/envs/py36/bin/python
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2
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3 #$ -S /home/jjjjia/.conda/envs/py36/bin/python
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4 #$ -V # Pass environment variables to the job
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5 #$ -N CPO_pipeline # Replace with a more specific job name
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6 #$ -wd /home/jjjjia/testCases # Use the current working dir
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7 #$ -pe smp 8 # Parallel Environment (how many cores)
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8 #$ -l h_vmem=11G # Memory (RAM) allocation *per core*
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9 #$ -e ./logs/$JOB_ID.err
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10 #$ -o ./logs/$JOB_ID.log
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11 #$ -m ea
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12 #$ -M bja20@sfu.ca
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13
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3
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14 #./prediction.py -i ~/testCases/cpoResults/contigs/BC11-Kpn005_S2.fa -m ~/testCases/predictionResultsQsubTest/predictions/BC11-Kpn005_S2.mlst -c ~/testCases/predictionResultsQsubTest/predictions/BC11-Kpn005_S2.recon/contig_report.txt -f ~/testCases/predictionResultsQsubTest/predictions/BC11-Kpn005_S2.recon/mobtyper_aggregate_report.txt -a ~/testCases/predictionResultsQsubTest/predictions/BC11-Kpn005_S2.cp -r ~/testCases/predictionResultsQsubTest/predictions/BC11-Kpn005_S2.rgi.txt -e "Klebsiella"
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15 import subprocess
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16 import pandas
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17 import optparse
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18 import os
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19 import datetime
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20 import sys
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21 import time
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22 import urllib.request
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23 import gzip
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24 import collections
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25 import json
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26 import numpy
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27
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28
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6
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29 debug = False #debug skips the shell scripts and also dump out a ton of debugging messages
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30
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31 if not debug:
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32 #parses some parameters
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33 parser = optparse.OptionParser("Usage: %prog [options] arg1 arg2 ...")
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34 #required
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3
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35 #MLSTHIT, mobsuite, resfinder, rgi, mlstscheme
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36 parser.add_option("-i", "--id", dest="id", type="string", help="identifier of the isolate")
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3
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37 parser.add_option("-m", "--mlst", dest="mlst", type="string", help="absolute file path to mlst result")
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38 parser.add_option("-c", "--mobfinderContig", dest="mobfinderContig", type="string", help="absolute path to mobfinder aggregate result")
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39 parser.add_option("-f", "--mobfinderAggregate", dest="mobfinderAggregate", type="string", help="absolute path to mobfinder plasmid results")
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40 parser.add_option("-a", "--abricate", dest="abricate", type="string", help="absolute path to abricate results")
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41 parser.add_option("-r", "--rgi", dest="rgi", type="string", help="absolute path to rgi results")
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42 parser.add_option("-e", "--expected", dest="expectedSpecies", default="NA/NA/NA", type="string", help="expected species of the isolate")
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43 parser.add_option("-s", "--mlst-scheme", dest="mlstScheme", default= "./scheme_species_map.tab", type="string", help="absolute file path to mlst scheme")
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44 parser.add_option("-p", "--plasmidfinder", dest="plasmidfinder", type="string", help="absolute file path to plasmidfinder ")
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45
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46 #parallelization, useless, these are hard coded to 8cores/64G RAM
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47 #parser.add_option("-t", "--threads", dest="threads", default=8, type="int", help="number of cpu to use")
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48 #parser.add_option("-p", "--memory", dest="memory", default=64, type="int", help="memory to use in GB")
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49
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50 (options,args) = parser.parse_args()
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51 #if len(args) != 8:
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52 #parser.error("incorrect number of arguments, all 7 is required")
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53 curDir = os.getcwd()
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3
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54 ID = str(options.id).lstrip().rstrip()
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55 mlst = str(options.mlst).lstrip().rstrip()
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56 mobfindercontig = str(options.mobfinderContig).lstrip().rstrip()
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57 mobfinderaggregate = str(options.mobfinderAggregate).lstrip().rstrip()
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58 abricate = str(options.abricate).lstrip().rstrip()
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59 rgi = str(options.rgi).lstrip().rstrip()
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60 expectedSpecies = str(options.expectedSpecies).lstrip().rstrip()
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61 mlstScheme = str(options.mlstScheme).lstrip().rstrip()
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62 plasmidfinder = str(options.plasmidfinder).lstrip().rstrip()
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63 outputDir = "./"
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64 print(mlst)
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65 print(mobfindercontig)
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66 print(mobfinderaggregate)
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67 print(abricate)
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68 print(rgi)
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69 print(expectedSpecies)
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70 print(mlstScheme)
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71 else:
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72 curDir = os.getcwd()
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73 ID = "BC11"
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74 mlst = "D:\OneDrive\ProjectCDC\ProjectCDCInPython\ProjectCDCInPython\pipelineTest\predictions\BC11-Kpn005_S2.mlst"
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75 mobfindercontig = "D:\OneDrive\ProjectCDC\ProjectCDCInPython\ProjectCDCInPython\pipelineTest\predictions\BC11-Kpn005_S2.recon\contig_report.txt"
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76 mobfinderaggregate = "D:\OneDrive\ProjectCDC\ProjectCDCInPython\ProjectCDCInPython\pipelineTest\predictions\BC11-Kpn005_S2.recon\mobtyper_aggregate_report.txt"
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77 abricate = "D:\OneDrive\ProjectCDC\ProjectCDCInPython\ProjectCDCInPython\pipelineTest\predictions\BC11-Kpn005_S2.cp"
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78 rgi = "D:\OneDrive\ProjectCDC\ProjectCDCInPython\ProjectCDCInPython\pipelineTest\predictions\BC11-Kpn005_S2.rgi.txt"
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79 expectedSpecies = "Escherichia coli"
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80 mlstScheme = "D:\OneDrive\ProjectCDC\ProjectCDCInPython\ProjectCDCInPython\pipelineTest\scheme_species_map.tab"
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81 plasmidfinder = "D:\OneDrive\ProjectCDC\ProjectCDCInPython\ProjectCDCInPython\pipelineTest\predictions\BC11-Kpn005_S2.origins"
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82 outputDir = "./"
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1
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83
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84 #region result objects
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85 #define some objects to store values from results
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86 #//TODO this is not the proper way of get/set private object variables. every value has manually assigned defaults intead of specified in init(). Also, use property(def getVar, def setVar).
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87 class starFinders(object):
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88 def __init__(self):
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89 self.file = ""
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90 self.sequence = ""
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91 self.start = 0
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92 self.end = 0
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93 self.gene = ""
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94 self.shortGene = ""
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95 self.coverage = ""
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96 self.coverage_map = ""
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97 self.gaps = ""
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98 self.pCoverage = 100.00
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99 self.pIdentity = 100.00
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100 self.database = ""
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101 self.accession = ""
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102 self.product = ""
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103 self.source = "chromosome"
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104 self.row = ""
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105
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106 class PlasFlowResult(object):
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107 def __init__(self):
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108 self.sequence = ""
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109 self.length = 0
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110 self.label = ""
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111 self.confidence = 0
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112 self.usefulRow = ""
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113 self.row = ""
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114
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115 class MlstResult(object):
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116 def __init__(self):
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117 self.file = ""
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118 self.speciesID = ""
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119 self.seqType = 0
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120 self.scheme = ""
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121 self.species = ""
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122 self.row=""
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123
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124 class mobsuiteResult(object):
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125 def __init__(self):
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126 self.file_id = ""
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127 self.cluster_id = ""
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128 self.contig_id = ""
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129 self.contig_num = 0
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130 self.contig_length = 0
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131 self.circularity_status = ""
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132 self.rep_type = ""
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133 self.rep_type_accession = ""
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134 self.relaxase_type = ""
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135 self.relaxase_type_accession = ""
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136 self.mash_nearest_neighbor = ""
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137 self.mash_neighbor_distance = 0.00
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138 self.repetitive_dna_id = ""
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139 self.match_type = ""
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140 self.score = 0
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141 self.contig_match_start = 0
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142 self.contig_match_end = 0
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143 self.row = ""
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144
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145 class mobsuitePlasmids(object):
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146 def __init__(self):
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147 self.file_id = ""
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148 self.num_contigs = 0
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149 self.total_length = 0
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150 self.gc = ""
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151 self.rep_types = ""
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152 self.rep_typeAccession = ""
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153 self.relaxase_type= ""
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154 self.relaxase_type_accession = ""
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155 self.mpf_type = ""
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156 self.mpf_type_accession= ""
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157 self.orit_type = ""
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158 self.orit_accession = ""
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159 self.PredictedMobility = ""
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160 self.mash_nearest_neighbor = ""
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161 self.mash_neighbor_distance = 0.00
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162 self.mash_neighbor_cluster= 0
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163 self.row = ""
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3
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164
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165 class RGIResult(object):
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166 def __init__(self):
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167 self.ORF_ID = ""
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168 self.Contig = ""
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169 self.Start = -1
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170 self.Stop = -1
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171 self.Orientation = ""
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172 self.Cut_Off = ""
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173 self.Pass_Bitscore = 100000
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174 self.Best_Hit_Bitscore = 0.00
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175 self.Best_Hit_ARO = ""
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176 self.Best_Identities = 0.00
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177 self.ARO = 0
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178 self.Model_type = ""
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179 self.SNPs_in_Best_Hit_ARO = ""
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180 self.Other_SNPs = ""
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181 self.Drug_Class = ""
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182 self.Resistance_Mechanism = ""
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183 self.AMR_Gene_Family = ""
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184 self.Predicted_DNA = ""
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185 self.Predicted_Protein = ""
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186 self.CARD_Protein_Sequence = ""
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187 self.Percentage_Length_of_Reference_Sequence = 0.00
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188 self.ID = ""
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189 self.Model_ID = 0
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190 self.source = ""
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191 self.row = ""
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192
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193 #endregion
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194
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195 #region useful functions
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196 def read(path):
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197 return [line.rstrip('\n') for line in open(path)]
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198 def execute(command):
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199 process = subprocess.Popen(command, shell=False, cwd=curDir, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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200
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201 # Poll process for new output until finished
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202 while True:
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203 nextline = process.stdout.readline()
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204 if nextline == '' and process.poll() is not None:
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205 break
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206 sys.stdout.write(nextline)
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207 sys.stdout.flush()
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208
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209 output = process.communicate()[0]
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210 exitCode = process.returncode
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211
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212 if (exitCode == 0):
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213 return output
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214 else:
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215 raise subprocess.CalledProcessError(exitCode, command)
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216 def httpGetFile(url, filepath=""):
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217 if (filepath == ""):
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218 return urllib.request.urlretrieve(url)
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219 else:
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220 urllib.request.urlretrieve(url, filepath)
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221 return True
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222 def gunzip(inputpath="", outputpath=""):
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223 if (outputpath == ""):
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224 with gzip.open(inputpath, 'rb') as f:
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225 gzContent = f.read()
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226 return gzContent
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227 else:
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228 with gzip.open(inputpath, 'rb') as f:
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229 gzContent = f.read()
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230 with open(outputpath, 'wb') as out:
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231 out.write(gzContent)
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232 return True
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233 def ToJson(dictObject, outputPath):
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234 #outDir = outputDir + '/summary/' + ID + ".json/"
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235 #if not (os.path.exists(outDir)):
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236 #os.makedirs(outDir)
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237 #with open(outputPath, 'w') as f:
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238 #json.dump([ob.__dict__ for ob in dictObject.values()], f, ensure_ascii=False)
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239 return ""
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1
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240 #endregion
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241
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242 #region functions to parse result files
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243 def ParseMLSTResult(pathToMLSTResult, scheme):
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244 _mlstResult = {}
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245 scheme = pandas.read_csv(scheme, delimiter='\t', header=0)
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246 scheme = scheme.replace(numpy.nan, '', regex=True)
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247
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248 taxon = {}
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249 #record the scheme as a dictionary
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250 taxon["-"] = "No MLST Match"
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251 for i in range(len(scheme.index)):
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252 key = scheme.iloc[i,0]
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253 if (str(scheme.iloc[i,2]) == "nan"):
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254 value = str(scheme.iloc[i,1])
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255 else:
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256 value = str(scheme.iloc[i,1]) + " " + str(scheme.iloc[i,2])
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257
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258 if (key in taxon.keys()):
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259 taxon[key] = taxon.get(key) + ";" + value
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260 else:
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261 taxon[key] = value
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262 #read in the mlst result
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263 mlst = pandas.read_csv(pathToMLSTResult, delimiter='\t', header=None)
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264 _mlstHit = MlstResult()
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265
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266 _mlstHit.file = mlst.iloc[0,0]
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267 _mlstHit.speciesID = (mlst.iloc[0,1])
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268 _mlstHit.seqType = str(mlst.iloc[0,2])
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269 for i in range(3, len(mlst.columns)):
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270 _mlstHit.scheme += mlst.iloc[0,i] + ";"
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271 _mlstHit.species = taxon[_mlstHit.speciesID]
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272 _mlstHit.row = "\t".join(str(x) for x in mlst.ix[0].tolist())
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273 _mlstResult[_mlstHit.speciesID]=_mlstHit
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274
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275 return _mlstResult
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276
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277 def ParsePlasmidFinderResult(pathToPlasmidFinderResult):
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278 #pipelineTest/contigs/BC110-Kpn005.fa contig00019 45455 45758 IncFIC(FII)_1 8-308/499 ========/=..... 8/11 59.52 75.65 plasmidfinder AP001918 IncFIC(FII)_1__AP001918
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279 #example resfinder:
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280 #pipelineTest/contigs/BC110-Kpn005.fa contig00038 256 1053 OXA-181 1-798/798 =============== 0/0 100.00 100.00 bccdc AEP16366.1 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-181
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281
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282 _pFinder = {} #***********************
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283 plasmidFinder = pandas.read_csv(pathToPlasmidFinderResult, delimiter='\t', header=0)
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284 plasmidFinder = plasmidFinder.replace(numpy.nan, '', regex=True)
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285
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286
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287 for i in range(len(plasmidFinder.index)):
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288 pf = starFinders()
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289 pf.file = str(plasmidFinder.iloc[i,0])
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290 pf.sequence = str(plasmidFinder.iloc[i,1])
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291 pf.start = int(plasmidFinder.iloc[i,2])
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292 pf.end = int(plasmidFinder.iloc[i,3])
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293 pf.gene = str(plasmidFinder.iloc[i,4])
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294 pf.shortGene = pf.gene[:pf.gene.index("_")]
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295 pf.coverage = str(plasmidFinder.iloc[i,5])
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296 pf.coverage_map = str(plasmidFinder.iloc[i,6])
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297 pf.gaps = str(plasmidFinder.iloc[i,7])
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298 pf.pCoverage = float(plasmidFinder.iloc[i,8])
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299 pf.pIdentity = float(plasmidFinder.iloc[i,9])
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300 pf.database = str(plasmidFinder.iloc[i,10])
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301 pf.accession = str(plasmidFinder.iloc[i,11])
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302 pf.product = str(plasmidFinder.iloc[i,12])
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303 pf.source = "plasmid"
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304 pf.row = "\t".join(str(x) for x in plasmidFinder.ix[i].tolist())
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305 _pFinder[pf.gene]=pf
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306 #row = "\t".join(str(x) for x in plasmidFinder.ix[i].tolist())
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307 #plasmidFinderContigs.append(str(plasmidFinder.iloc[i,1]))
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308 #origins.append(str(plasmidFinder.iloc[i,4][:plasmidFinder.iloc[i,4].index("_")]))
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309 return _pFinder
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310
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311 def ParseMobsuiteResult(pathToMobsuiteResult):
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312 _mobsuite = {}
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313 mResult = pandas.read_csv(pathToMobsuiteResult, delimiter='\t', header=0)
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314 mResult = mResult.replace(numpy.nan, '', regex=True)
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315
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316 for i in range(len(mResult.index)):
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317 mr = mobsuiteResult()
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318 mr.file_id = str(mResult.iloc[i,0])
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319 mr.cluster_id = str(mResult.iloc[i,1])
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320 if (mr.cluster_id == "chromosome"):
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321 break
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322 mr.contig_id = str(mResult.iloc[i,2])
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323 mr.contig_num = mr.contig_id[(mr.contig_id.find("contig")+6):mr.contig_id.find("_len=")]
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324 mr.contig_length = int(mResult.iloc[i,3])
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325 mr.circularity_status = str(mResult.iloc[i,4])
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326 mr.rep_type = str(mResult.iloc[i,5])
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327 mr.rep_type_accession = str(mResult.iloc[i,6])
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328 mr.relaxase_type = str(mResult.iloc[i,7])
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329 mr.relaxase_type_accession = str(mResult.iloc[i,8])
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330 mr.mash_nearest_neighbor = str(mResult.iloc[i,9])
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331 mr.mash_neighbor_distance = float(mResult.iloc[i,10])
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332 mr.repetitive_dna_id = str(mResult.iloc[i,11])
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333 mr.match_type = str(mResult.iloc[i,12])
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334 if (mr.match_type == ""):
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335 mr.score = -1
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336 mr.contig_match_start = -1
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337 mr.contig_match_end = -1
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338 else:
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339 mr.score = int(mResult.iloc[i,13])
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340 mr.contig_match_start = int(mResult.iloc[i,14])
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341 mr.contig_match_end = int(mResult.iloc[i,15])
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342 mr.row = "\t".join(str(x) for x in mResult.ix[i].tolist())
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343 _mobsuite[mr.contig_id]=(mr)
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344 return _mobsuite
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345
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346 def ParseMobsuitePlasmids(pathToMobsuiteResult):
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347 _mobsuite = {}
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348 mResults = pandas.read_csv(pathToMobsuiteResult, delimiter='\t', header=0)
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349 mResults = mResults.replace(numpy.nan, '', regex=True)
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350
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351 for i in range(len(mResults.index)):
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352 mr = mobsuitePlasmids()
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353 mr.file_id = str(mResults.iloc[i,0])
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354 mr.num_contigs = int(mResults.iloc[i,1])
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355 mr.total_length = int(mResults.iloc[i,2])
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356 mr.gc = int(mResults.iloc[i,3])
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357 mr.rep_types = str(mResults.iloc[i,4])
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358 mr.rep_typeAccession = str(mResults.iloc[i,5])
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359 mr.relaxase_type = str(mResults.iloc[i,6])
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360 mr.relaxase_type_accession = str(mResults.iloc[i,7])
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361 mr.mpf_type = str(mResults.iloc[i,8])
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362 mr.mpf_type_accession = str(mResults.iloc[i,9])
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363 mr.orit_type = str(mResults.iloc[i,10])
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364 mr.orit_accession = str(mResults.iloc[i,11])
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365 mr.PredictedMobility = str(mResults.iloc[i,12])
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366 mr.mash_nearest_neighbor = str(mResults.iloc[i,13])
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367 mr.mash_neighbor_distance = float(mResults.iloc[i,14])
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368 mr.mash_neighbor_cluster = int(mResults.iloc[i,15])
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369 mr.row = "\t".join(str(x) for x in mResults.ix[i].tolist())
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370 _mobsuite[mr.file_id] = mr
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371 return _mobsuite
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|
|
372
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373 def ParseResFinderResult(pathToResFinderResults, plasmidContigs, likelyPlasmidContigs):
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374 _rFinder = {}
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375 resFinder = pandas.read_csv(pathToResFinderResults, delimiter='\t', header=0)
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376 resFinder = resFinder.replace(numpy.nan, '', regex=True)
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377
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378 for i in range(len(resFinder.index)):
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379 rf = starFinders()
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380 rf.file = str(resFinder.iloc[i,0])
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|
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381 rf.sequence = str(resFinder.iloc[i,1])
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382 rf.start = int(resFinder.iloc[i,2])
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|
383 rf.end = int(resFinder.iloc[i,3])
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384 rf.gene = str(resFinder.iloc[i,4])
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385 rf.shortGene = rf.gene
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386 rf.coverage = str(resFinder.iloc[i,5])
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387 rf.coverage_map = str(resFinder.iloc[i,6])
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388 rf.gaps = str(resFinder.iloc[i,7])
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|
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389 rf.pCoverage = float(resFinder.iloc[i,8])
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|
|
390 rf.pIdentity = float(resFinder.iloc[i,9])
|
|
|
391 rf.database = str(resFinder.iloc[i,10])
|
|
|
392 rf.accession = str(resFinder.iloc[i,11])
|
|
|
393 rf.product = str(resFinder.iloc[i,12])
|
|
|
394 rf.row = "\t".join(str(x) for x in resFinder.ix[i].tolist())
|
|
|
395 if (rf.sequence[6:] in plasmidContigs):
|
|
|
396 rf.source = "plasmid"
|
|
|
397 elif (rf.sequence[6:] in likelyPlasmidContigs):
|
|
|
398 rf.source = "likely plasmid"
|
|
|
399 else:
|
|
|
400 rf.source = "likely chromosome"
|
|
|
401 _rFinder[rf.gene]=rf
|
|
|
402 return _rFinder
|
|
|
403
|
|
|
404 def ParseRGIResult(pathToRGIResults, plasmidContigs, likelyPlasmidContigs):
|
|
|
405 _rgiR = {}
|
|
|
406 RGI = pandas.read_csv(pathToRGIResults, delimiter='\t', header=0)
|
|
|
407 RGI = RGI.replace(numpy.nan, '', regex=True)
|
|
|
408
|
|
|
409 for i in range(len(RGI.index)):
|
|
|
410 r = RGIResult()
|
|
|
411 r.ORF_ID = str(RGI.iloc[i,0])
|
|
|
412 r.Contig = str(RGI.iloc[i,1])
|
|
|
413 r.Contig_Num = r.Contig[6:r.Contig.find("_")]
|
|
|
414 r.Start = int(RGI.iloc[i,2])
|
|
|
415 r.Stop = int(RGI.iloc[i,3])
|
|
|
416 r.Orientation = str(RGI.iloc[i,4])
|
|
|
417 r.Cut_Off = str(RGI.iloc[i,5])
|
|
|
418 r.Pass_Bitscore = int(RGI.iloc[i,6])
|
|
|
419 r.Best_Hit_Bitscore = float(RGI.iloc[i,7])
|
|
|
420 r.Best_Hit_ARO = str(RGI.iloc[i,8])
|
|
|
421 r.Best_Identities = float(RGI.iloc[i,9])
|
|
|
422 r.ARO = int(RGI.iloc[i,10])
|
|
|
423 r.Model_type = str(RGI.iloc[i,11])
|
|
|
424 r.SNPs_in_Best_Hit_ARO = str(RGI.iloc[i,12])
|
|
|
425 r.Other_SNPs = str(RGI.iloc[i,13])
|
|
|
426 r.Drug_Class = str(RGI.iloc[i,14])
|
|
|
427 r.Resistance_Mechanism = str(RGI.iloc[i,15])
|
|
|
428 r.AMR_Gene_Family = str(RGI.iloc[i,16])
|
|
|
429 r.Predicted_DNA = str(RGI.iloc[i,17])
|
|
|
430 r.Predicted_Protein = str(RGI.iloc[i,18])
|
|
|
431 r.CARD_Protein_Sequence = str(RGI.iloc[i,19])
|
|
|
432 r.Percentage_Length_of_Reference_Sequence = float(RGI.iloc[i,20])
|
|
|
433 r.ID = str(RGI.iloc[i,21])
|
|
|
434 r.Model_ID = int(RGI.iloc[i,22])
|
|
|
435 r.row = "\t".join(str(x) for x in RGI.ix[i].tolist())
|
|
|
436 if (r.Contig_Num in plasmidContigs):
|
|
|
437 r.source = "plasmid"
|
|
|
438 elif (r.Contig_Num in likelyPlasmidContigs):
|
|
|
439 r.source = "likely plasmid"
|
|
|
440 else:
|
|
|
441 r.source = "likely chromosome"
|
|
|
442 _rgiR[r.Model_ID]=r
|
|
|
443 return _rgiR
|
|
3
|
444
|
|
|
445 def ParsePlasmidFinderResult(pathToPlasmidFinderResult):
|
|
|
446 #pipelineTest/contigs/BC110-Kpn005.fa contig00019 45455 45758 IncFIC(FII)_1 8-308/499 ========/=..... 8/11 59.52 75.65 plasmidfinder AP001918 IncFIC(FII)_1__AP001918
|
|
|
447 #example resfinder:
|
|
|
448 #pipelineTest/contigs/BC110-Kpn005.fa contig00038 256 1053 OXA-181 1-798/798 =============== 0/0 100.00 100.00 bccdc AEP16366.1 OXA-48 family carbapenem-hydrolyzing class D beta-lactamase OXA-181
|
|
|
449
|
|
|
450 _pFinder = {} #***********************
|
|
|
451 plasmidFinder = pandas.read_csv(pathToPlasmidFinderResult, delimiter='\t', header=0)
|
|
|
452
|
|
|
453 for i in range(len(plasmidFinder.index)):
|
|
|
454 pf = starFinders()
|
|
|
455 pf.file = str(plasmidFinder.iloc[i,0])
|
|
|
456 pf.sequence = str(plasmidFinder.iloc[i,1])
|
|
|
457 pf.start = int(plasmidFinder.iloc[i,2])
|
|
|
458 pf.end = int(plasmidFinder.iloc[i,3])
|
|
|
459 pf.gene = str(plasmidFinder.iloc[i,4])
|
|
13
|
460 if (pf.gene.find("_") > -1):
|
|
|
461 pf.shortGene = pf.gene[:pf.gene.index("_")]
|
|
|
462 else:
|
|
|
463 pf.shortGene = pf.gene
|
|
3
|
464 pf.coverage = str(plasmidFinder.iloc[i,5])
|
|
|
465 pf.coverage_map = str(plasmidFinder.iloc[i,6])
|
|
|
466 pf.gaps = str(plasmidFinder.iloc[i,7])
|
|
|
467 pf.pCoverage = float(plasmidFinder.iloc[i,8])
|
|
|
468 pf.pIdentity = float(plasmidFinder.iloc[i,9])
|
|
|
469 pf.database = str(plasmidFinder.iloc[i,10])
|
|
|
470 pf.accession = str(plasmidFinder.iloc[i,11])
|
|
|
471 pf.product = str(plasmidFinder.iloc[i,12])
|
|
|
472 pf.source = "plasmid"
|
|
|
473 pf.row = "\t".join(str(x) for x in plasmidFinder.ix[i].tolist())
|
|
|
474 _pFinder[pf.gene]=pf
|
|
|
475 #row = "\t".join(str(x) for x in plasmidFinder.ix[i].tolist())
|
|
|
476 #plasmidFinderContigs.append(str(plasmidFinder.iloc[i,1]))
|
|
|
477 #origins.append(str(plasmidFinder.iloc[i,4][:plasmidFinder.iloc[i,4].index("_")]))
|
|
|
478 return _pFinder
|
|
1
|
479 #endregion
|
|
|
480
|
|
|
481 def Main():
|
|
3
|
482 outputDir = "./"
|
|
1
|
483 notes = []
|
|
|
484 #init the output list
|
|
|
485 output = []
|
|
|
486 jsonOutput = []
|
|
|
487
|
|
3
|
488 print(str(datetime.datetime.now()) + "\n\nID: " + ID + "\nAssembly: " + ID)
|
|
|
489 output.append(str(datetime.datetime.now()) + "\n\nID: " + ID + "\nAssembly: " + ID)
|
|
1
|
490
|
|
|
491 #region parse the mlst results
|
|
|
492 print("step 3: parsing mlst, plasmid, and amr results")
|
|
|
493
|
|
|
494 print("identifying MLST")
|
|
3
|
495 mlstHit = ParseMLSTResult(mlst, str(mlstScheme))#***********************
|
|
1
|
496 ToJson(mlstHit, "mlst.json") #write it to a json output
|
|
|
497 mlstHit = list(mlstHit.values())[0]
|
|
|
498
|
|
|
499 #endregion
|
|
|
500
|
|
|
501 #region parse mobsuite, resfinder and rgi results
|
|
|
502 print("identifying plasmid contigs and amr genes")
|
|
|
503
|
|
|
504 plasmidContigs = []
|
|
|
505 likelyPlasmidContigs = []
|
|
|
506 origins = []
|
|
|
507
|
|
|
508 #parse mobsuite results
|
|
3
|
509 mSuite = ParseMobsuiteResult(mobfindercontig) #outputDir + "/predictions/" + ID + ".recon/contig_report.txt")#*************
|
|
1
|
510 ToJson(mSuite, "mobsuite.json") #*************
|
|
3
|
511 mSuitePlasmids = ParseMobsuitePlasmids(mobfinderaggregate)#outputDir + "/predictions/" + ID + ".recon/mobtyper_aggregate_report.txt")#*************
|
|
1
|
512 ToJson(mSuitePlasmids, "mobsuitePlasmids.json") #*************
|
|
|
513
|
|
|
514 for key in mSuite:
|
|
|
515 if mSuite[key].contig_num not in plasmidContigs and mSuite[key].contig_num not in likelyPlasmidContigs:
|
|
|
516 if not (mSuite[key].rep_type == ''):
|
|
|
517 plasmidContigs.append(mSuite[key].contig_num)
|
|
|
518 else:
|
|
|
519 likelyPlasmidContigs.append(mSuite[key].contig_num)
|
|
|
520 for key in mSuite:
|
|
|
521 if mSuite[key].rep_type not in origins:
|
|
|
522 origins.append(mSuite[key].rep_type)
|
|
|
523
|
|
|
524 #parse resfinder AMR results
|
|
3
|
525 pFinder = ParsePlasmidFinderResult(plasmidfinder)
|
|
|
526 ToJson(pFinder, "origins.json")
|
|
|
527
|
|
|
528 rFinder = ParseResFinderResult(abricate, plasmidContigs, likelyPlasmidContigs)#outputDir + "/predictions/" + ID + ".cp", plasmidContigs, likelyPlasmidContigs) #**********************
|
|
1
|
529 ToJson(rFinder, "resfinder.json") #*************
|
|
|
530
|
|
3
|
531 rgiAMR = ParseRGIResult(rgi, plasmidContigs, likelyPlasmidContigs) # outputDir + "/predictions/" + ID + ".rgi.txt", plasmidContigs, likelyPlasmidContigs)#***********************
|
|
1
|
532 ToJson(rgiAMR, "rgi.json") #*************
|
|
|
533
|
|
13
|
534 carbapenamases = []
|
|
|
535 resfinderCarbas = [] #list of rfinder objects for lindaout list
|
|
1
|
536 amrGenes = []
|
|
|
537 for keys in rFinder:
|
|
|
538 carbapenamases.append(rFinder[keys].shortGene + "(" + rFinder[keys].source + ")")
|
|
13
|
539 resfinderCarbas.append(rFinder[keys])
|
|
1
|
540 for keys in rgiAMR:
|
|
13
|
541 if (rgiAMR[keys].Drug_Class.find("carbapenem") > -1 and rgiAMR[keys].AMR_Gene_Family.find("beta-lactamase") > -1):
|
|
1
|
542 if (rgiAMR[keys].Best_Hit_ARO not in carbapenamases):
|
|
|
543 carbapenamases.append(rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")")
|
|
|
544 else:
|
|
|
545 if (rgiAMR[keys].Best_Hit_ARO not in amrGenes):
|
|
|
546 amrGenes.append(rgiAMR[keys].Best_Hit_ARO+ "(" + rgiAMR[keys].source + ")")
|
|
|
547 #endregion
|
|
|
548
|
|
|
549 #region output parsed mlst information
|
|
|
550 print("formatting mlst outputs")
|
|
|
551 output.append("\n\n\n~~~~~~~MLST summary~~~~~~~")
|
|
|
552 output.append("MLST determined species: " + mlstHit.species)
|
|
|
553 output.append("\nMLST Details: ")
|
|
|
554 output.append(mlstHit.row)
|
|
|
555
|
|
|
556 output.append("\nMLST information: ")
|
|
|
557 if (mlstHit.species == expectedSpecies):
|
|
|
558 output.append("MLST determined species is the same as expected species")
|
|
|
559 #notes.append("MLST determined species is the same as expected species")
|
|
|
560 else:
|
|
|
561 output.append("!!!MLST determined species is NOT the same as expected species, contamination? mislabeling?")
|
|
|
562 notes.append("MLST: Not expected species. Possible contamination or mislabeling")
|
|
|
563
|
|
|
564 #endregion
|
|
|
565
|
|
|
566 #region output the parsed plasmid/amr results
|
|
|
567 output.append("\n\n\n~~~~~~~~Plasmids~~~~~~~~\n")
|
|
|
568
|
|
|
569 output.append("predicted plasmid origins: ")
|
|
|
570 output.append(";".join(origins))
|
|
|
571
|
|
|
572 output.append("\ndefinitely plasmid contigs")
|
|
|
573 output.append(";".join(plasmidContigs))
|
|
|
574
|
|
|
575 output.append("\nlikely plasmid contigs")
|
|
|
576 output.append(";".join(likelyPlasmidContigs))
|
|
|
577
|
|
|
578 output.append("\nmob-suite prediction details: ")
|
|
|
579 for key in mSuite:
|
|
|
580 output.append(mSuite[key].row)
|
|
|
581
|
|
|
582 output.append("\n\n\n~~~~~~~~AMR Genes~~~~~~~~\n")
|
|
|
583 output.append("predicted carbapenamase Genes: ")
|
|
|
584 output.append(",".join(carbapenamases))
|
|
|
585 output.append("other RGI AMR Genes: ")
|
|
|
586 for key in rgiAMR:
|
|
|
587 output.append(rgiAMR[key].Best_Hit_ARO + "(" + rgiAMR[key].source + ")")
|
|
|
588
|
|
|
589 output.append("\nDetails about the carbapenamase Genes: ")
|
|
|
590 for key in rFinder:
|
|
|
591 output.append(rFinder[key].row)
|
|
|
592 output.append("\nDetails about the RGI AMR Genes: ")
|
|
|
593 for key in rgiAMR:
|
|
|
594 output.append(rgiAMR[key].row)
|
|
|
595
|
|
|
596 #write summary to a file
|
|
|
597 summaryDir = outputDir + "/summary/" + ID
|
|
3
|
598 out = open("summary.txt", 'w')
|
|
1
|
599 for item in output:
|
|
|
600 out.write("%s\n" % item)
|
|
|
601
|
|
|
602
|
|
|
603 #TSV output
|
|
6
|
604 lindaOut = []
|
|
1
|
605 tsvOut = []
|
|
13
|
606 lindaOut.append("ID\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_2_RFLP\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")
|
|
|
607 lindaTemp = ID + "\t" #id
|
|
|
608 lindaTemp += "\t" #quality
|
|
|
609 lindaTemp += expectedSpecies + "\t" #expected
|
|
|
610 lindaTemp += mlstHit.species + "\t" #mlstscheme
|
|
|
611 lindaTemp += str(mlstHit.seqType) + "\t" #seq type
|
|
|
612 lindaTemp += "\t".join(mlstHit.scheme.split(";")) + "\t"#mlst alleles x 7
|
|
|
613 lindaTemp += "\t\t" #sero and kcap
|
|
|
614
|
|
|
615 #resfinderCarbas
|
|
|
616 for carbs in resfinderCarbas:
|
|
|
617 if (carbs.source == "plasmid"): #
|
|
|
618 lindaTemp += "\t\t\t\t\t" #plasmid 1 rflp plasmid 1 family information. PLASMID_1_FAMILY\tPLASMID_1_BEST_MATCH\tPLASMID_1_COVERAGE\tPLASMID_1_SNVS_TO_BEST_MATCH
|
|
|
619 lindaTemp += carbs.shortGene + "\t" #found an carbapenase
|
|
|
620 contig = carbs.sequence[6:] #this is the contig number
|
|
|
621 for i in mSuite.keys():
|
|
|
622 if (str(mSuite[i].contig_num) == str(contig)): #found the right plasmid
|
|
|
623 lindaTemp += mSuite[i].rep_type
|
|
|
624 lindaOut.append(lindaTemp)
|
|
|
625 out = open("summary.linda.tsv", 'w')
|
|
|
626 for item in lindaOut:
|
|
|
627 out.write("%s\n" % item)
|
|
6
|
628
|
|
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629 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")
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1
|
630 #start with ID
|
|
6
|
631 temp = "\t"
|
|
1
|
632 temp += (ID + "\t")
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|
|
633 temp += expectedSpecies + "\t"
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634
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635 #move into MLST
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636 temp += mlstHit.species + "\t"
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637 temp += str(mlstHit.seqType) + "\t"
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|
638 temp += mlstHit.scheme + "\t"
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639
|
|
|
640 #now onto AMR genes
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|
|
641 temp += ";".join(carbapenamases) + "\t"
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|
642 temp += ";".join(amrGenes) + "\t"
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|
|
643
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|
|
644 #lastly plasmids
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|
|
645 temp+= str(len(mSuitePlasmids)) + "\t"
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646 plasmidID = ""
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|
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647 contigs = ""
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648 lengths = ""
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|
|
649 rep_type = ""
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|
|
650 mobility = ""
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|
|
651 neighbour = ""
|
|
|
652 for keys in mSuitePlasmids:
|
|
|
653 plasmidID += str(mSuitePlasmids[keys].mash_neighbor_cluster) + ";"
|
|
|
654 contigs += str(mSuitePlasmids[keys].num_contigs) + ";"
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|
|
655 lengths += str(mSuitePlasmids[keys].total_length) + ";"
|
|
|
656 rep_type += str(mSuitePlasmids[keys].rep_types) + ";"
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|
|
657 mobility += str(mSuitePlasmids[keys].PredictedMobility) + ";"
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|
|
658 neighbour += str(mSuitePlasmids[keys].mash_nearest_neighbor) + ";"
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|
|
659 temp += plasmidID + "\t" + contigs + "\t" + lengths + "\t" + rep_type + "\t" + mobility + "\t" + neighbour + "\t"
|
|
|
660 temp += ";".join(plasmidContigs) + "\t"
|
|
|
661 temp += ";".join(likelyPlasmidContigs)
|
|
|
662 tsvOut.append(temp)
|
|
|
663
|
|
|
664 summaryDir = outputDir + "/summary/" + ID
|
|
3
|
665 out = open("summary.tsv", 'w')
|
|
1
|
666 for item in tsvOut:
|
|
|
667 out.write("%s\n" % item)
|
|
|
668 #endregion
|
|
|
669
|
|
|
670
|
|
|
671 start = time.time()#time the analysis
|
|
|
672 print("Starting workflow...")
|
|
|
673 #analysis time
|
|
|
674 Main()
|
|
|
675
|
|
|
676 end = time.time()
|
|
5
|
677 print("Finished!\nThe analysis used: " + str(end-start) + " seconds") |
