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1 #! /usr/bin/env python
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2 #
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3 # Copyright INRA-URGI 2009-2010
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4 #
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5 # This software is governed by the CeCILL license under French law and
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31 """Merge elements of two transcript lists with some condition"""
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32
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33 import os, random, shutil, glob
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34 from optparse import OptionParser
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35 from commons.core.parsing.SequenceListParser import SequenceListParser
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36 from commons.core.parsing.BedParser import BedParser
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37 from commons.core.parsing.GffParser import GffParser
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38 from commons.core.writer.TranscriptWriter import TranscriptWriter
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39 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
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40 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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41 from SMART.Java.Python.misc.RPlotter import RPlotter
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42 from SMART.Java.Python.misc.Progress import Progress
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43
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44
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45
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46 class MergeLists(object):
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47
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48 def __init__(self, verbosity):
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49 self.verbosity = verbosity
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50 self.seed = random.randint(0, 100000)
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51 self.aggregation = False
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52 self.normalization = False
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53 self.distance = False
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54 self.antisense = False
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55 self.colinear = False
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56 self.fileNames = {}
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57 self.formats = {}
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58 self.tmpFileNames = []
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59 self.logHandle = None
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60
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61 # def __del__(self):
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62 # for fileNameRoot in self.tmpFileNames:
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63 # for fileName in glob.glob("%s*" % (fileNameRoot)):
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64 # os.remove(fileName)
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65 # if self.logHandle != None:
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66 # self.logHandle.close()
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67 # self.logHandle = None
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68
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69 def setLogFileName(self, fileName):
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70 self.logHandle = open(fileName, "w")
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71
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72 def setInputFileName(self, fileName, format, id):
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73 self.fileNames[id] = fileName
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74 self.formats[id] = format
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75
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76 def setOutputFileName(self, fileName):
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77 self.outputFileName = fileName
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78
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79 def setAggregate(self, aggregation):
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80 self.aggregation = aggregation
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81
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82 def setNormalization(self, normalization):
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83 self.normalization = normalization
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84
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85 def setDistance(self, distance):
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86 self.distance = distance
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87
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88 def setAntisense(self, antisense):
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89 self.antisense = antisense
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90
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91 def setColinear(self, colinear):
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92 self.colinear = colinear
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93
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94 def createTmpFileName(self, root):
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95 fileName = "tmp_%s_%d.gff3" % (root, self.seed)
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96 self.tmpFileNames.append(fileName)
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97 return fileName
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98
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99 def selfMerge(self, fileName, format, outputFileName):
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100 transcriptListComparator = TranscriptListsComparator(self.logHandle, self.verbosity)
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101 transcriptListComparator.getColinearOnly(True)
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102 transcriptListComparator.setNormalization(self.normalization)
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103 transcriptContainer = TranscriptContainer(fileName, format, self.verbosity)
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104 writer = TranscriptWriter(outputFileName, "gff3", self.verbosity)
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105 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer)
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106 transcriptListComparator.setOutputWriter(writer)
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107 transcriptListComparator.compareTranscriptListSelfMerge()
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108
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109 def keepOverlapping(self, fileNames, formats, outputFileName):
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110 transcriptListComparator = TranscriptListsComparator(self.logHandle, self.verbosity)
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111 transcriptListComparator.getAntisenseOnly(self.antisense)
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112 transcriptListComparator.getColinearOnly(self.colinear)
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113 for i in (0, 1):
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114 transcriptContainer = TranscriptContainer(fileNames[i], formats[i], self.verbosity)
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115 transcriptListComparator.setInputTranscriptContainer(i, transcriptContainer)
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116 transcriptListComparator.aggregate(self.aggregation)
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117 transcriptListComparator.setNormalization(self.normalization)
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118 transcriptListComparator.setMaxDistance(self.distance)
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119 writer = TranscriptWriter(outputFileName, "gff3", self.verbosity)
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120 transcriptListComparator.setOutputWriter(writer)
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121 transcriptListComparator.compareTranscriptList()
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122
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123 def mergeFiles(self, fileName1, fileName2, outputFileName):
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124 outputFile = open(outputFileName, "w")
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125 shutil.copyfileobj(open(fileName1, "r"), outputFile)
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126 shutil.copyfileobj(open(fileName2, "r"), outputFile)
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127 outputFile.close()
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128
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129 def run(self):
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130 selectedFileQuery = self.createTmpFileName("query")
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131 self.keepOverlapping({0: self.fileNames[0], 1: self.fileNames[0]}, {0: "gff3", 1: "gff3"}, selectedFileQuery)
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132 mergeFileTarget = self.createTmpFileName("target")
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133 self.selfMerge(self.fileNames[1], self.formats[1], mergeFileTarget)
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134 if not self.aggregation:
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135 overlapFile = self.createTmpFileName("overlap")
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136 self.keepOverlapping({0: mergeFileTarget, 1: selectedFileQuery}, {0: "gff3", 1: "gff3"}, overlapFile)
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137 mergeFileTarget = overlapFile
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138 mergeFileMerged = self.createTmpFileName("merged")
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139 self.mergeFiles(mergeFileTarget, selectedFileQuery, mergeFileMerged)
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140 self.selfMerge(mergeFileMerged, "gff3", self.outputFileName)
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141
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142
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143
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144 if __name__ == "__main__":
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145
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146 # parse command line
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147 description = "Merge Lists v1.0.3: Merge the elements of two lists of genomic coordinates. [Category: Merge]"
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148
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149 parser = OptionParser(description = description)
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150 parser.add_option("-i", "--input1", dest="inputFileName1", action="store", type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
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151 parser.add_option("-f", "--format1", dest="format1", action="store", type="string", help="format of file 1 [compulsory] [format: transcript file format]")
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152 parser.add_option("-j", "--input2", dest="inputFileName2", action="store", default=None, type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
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153 parser.add_option("-g", "--format2", dest="format2", action="store", default=None, type="string", help="format of file 2 [compulsory] [format: file in transcript format]")
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154 parser.add_option("-o", "--output", dest="outputFileName", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
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155 parser.add_option("-k", "--all", dest="all", action="store_true", default=False, help="print all the transcripts, not only those overlapping [format: bool] [default: false]")
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156 parser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="max. distance between two transcripts [format: int] [default: 0]")
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157 parser.add_option("-a", "--antisense", dest="antisense", action="store_true", default=False, help="antisense only [format: bool] [default: false]")
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158 parser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False, help="colinear only [format: bool] [default: false]")
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159 parser.add_option("-n", "--normalize", dest="normalize", action="store_true", default=False, help="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]")
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160 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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161 (options, args) = parser.parse_args()
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162
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163 # ml = MergeLists(logHandle, options.verbosity)
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164
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165 ml = MergeLists(0)
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166 ml.setInputFileName(options.inputFileName1, options.format1, 0)
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167 ml.setInputFileName(options.inputFileName2, options.format2, 1)
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168 ml.setOutputFileName(options.outputFileName)
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169 ml.setAntisense(options.antisense)
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170 ml.setColinear(options.colinear)
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171 ml.setAggregate(options.all)
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172 ml.setNormalization(options.normalize)
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173 ml.setDistance(options.distance)
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174 ml.run()
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