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1 #!/usr/bin/env python
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2
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3 # Copyright INRA (Institut National de la Recherche Agronomique)
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4 # http://www.inra.fr
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5 # http://urgi.versailles.inra.fr
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6 #
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7 # This software is governed by the CeCILL license under French law and
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8 # abiding by the rules of distribution of free software. You can use,
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9 # modify and/ or redistribute the software under the terms of the CeCILL
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10 # license as circulated by CEA, CNRS and INRIA at the following URL
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11 # "http://www.cecill.info".
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12 #
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13 # As a counterpart to the access to the source code and rights to copy,
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14 # modify and redistribute granted by the license, users are provided only
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15 # with a limited warranty and the software's author, the holder of the
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16 # economic rights, and the successive licensors have only limited
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17 # liability.
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18 #
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19 # In this respect, the user's attention is drawn to the risks associated
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20 # with loading, using, modifying and/or developing or reproducing the
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21 # software by the user in light of its specific status of free software,
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22 # that may mean that it is complicated to manipulate, and that also
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23 # therefore means that it is reserved for developers and experienced
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24 # professionals having in-depth computer knowledge. Users are therefore
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25 # encouraged to load and test the software's suitability as regards their
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26 # requirements in conditions enabling the security of their systems and/or
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27 # data to be ensured and, more generally, to use and operate it in the
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28 # same conditions as regards security.
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29 #
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30 # The fact that you are presently reading this means that you have had
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31 # knowledge of the CeCILL license and that you accept its terms.
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32
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33 import os
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34 import sys
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35
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36 if not "REPET_PATH" in os.environ.keys():
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37 print "ERROR: no environment variable REPET_PATH"
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38 sys.exit(1)
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39 sys.path.append(os.environ["REPET_PATH"])
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40 if not "PYTHONPATH" in os.environ.keys():
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41 os.environ["PYTHONPATH"] = os.environ["REPET_PATH"]
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42 else:
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43 os.environ["PYTHONPATH"] = "%s:%s" % (os.environ["REPET_PATH"], os.environ["PYTHONPATH"])
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44
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45 from commons.core.LoggerFactory import LoggerFactory
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46 from commons.core.utils.RepetOptionParser import RepetOptionParser
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47 from commons.core.checker.ConfigChecker import ConfigRules
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48 from commons.core.checker.ConfigChecker import ConfigChecker
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49 from commons.core.seq.FastaUtils import FastaUtils
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50 from denovo_pipe.ReverseComplementAccordingToClassif import ReverseComplementAccordingToClassif
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51 from denovo_pipe.RenameHeaderClassif import RenameHeaderClassif
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52 from denovo_pipe.DetectTEFeatures import DetectTEFeatures
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53 from denovo_pipe.LaunchPASTEC import LaunchPASTEC
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54 from PASTEC.StatPastec import StatPastec
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55
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56 LOG_DEPTH = "repet.tools"
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57 #LOG_FORMAT = "%(message)s"
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58
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59 ####TEclassifier PASTEC Edition
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60 #
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61 class TEclassifierPE(object):
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62
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63 def __init__(self, fastaFileName = "", configFileName = "", addWickerCode = False, reverseComp = False, doClean = False, verbosity = 0):
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64 self._fastaFileName = fastaFileName
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65 self._addWickerCode = addWickerCode
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66 self._reverseComp = reverseComp
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67 self._configFileName = configFileName
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68 self._doClean = doClean
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69 self._verbosity = verbosity
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70 self._projectName = ""
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71 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
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72
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73 def setAttributesFromCmdLine(self):
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74 description = "TE classifier PASTEC Edition.\n"
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75 description += "Detect TE features on consensus and classify them. Give some classification statistics.\n"
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76 description += "Can rename headers with classification info and Wicker's code at the beginning.\n"
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77 description += "Can reverse-complement consensus if they are detected in reverse strand.\n"
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78 description += "Warning : it's highly advised to use sequences in upper case.\n"
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79 epilog = "\n"
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80 epilog += "Example 1: launch and clean temporary files\n"
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81 epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c\n"
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82 epilog += "\n"
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83 epilog += "Example 2: launch with 'rename headers' and 'reverse-complement' options\n"
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84 epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c -w -r\n"
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85 parser = RepetOptionParser(description = description, epilog = epilog)
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86 parser.add_option("-i", "--fasta", dest = "fastaFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
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87 parser.add_option("-C", "--config", dest = "configFileName",action = "store", type = "string", help = "configuration file name (e.g. TEclassifier.cfg) [compulsory]", default = "")
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88 parser.add_option("-w", "--wicker", dest = "addWickerCode", action = "store_true", help = "add classification info and Wicker's code at the beginning of the headers [optional] [default: False]", default = False)
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89 parser.add_option("-r", "--reverse", dest = "reverseComp", action = "store_true", help = "reverse-complement consensus if they are detected in reverse strand [optional] [default: False]", default = False)
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90 parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False)
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91 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 3, from 1 to 4]", default = 3)
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92 options = parser.parse_args()[0]
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93 self._setAttributesFromOptions(options)
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94
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95 def _setAttributesFromOptions(self, options):
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96 self.setFastaFileName(options.fastaFileName)
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97 self.setAddWickerCode(options.addWickerCode)
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98 self.setReverseComp(options.reverseComp)
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99 self.setConfigFileName(options.configFileName)
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100 self.setDoClean(options.doClean)
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101 self.setVerbosity(options.verbosity)
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102
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103 def _checkConfig(self):
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104 iConfigRules = ConfigRules()
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105 iConfigRules.addRuleOption(section="project", option ="project_name", mandatory=True, type="string")
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106 sectionName = "classif_consensus"
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107 iConfigRules.addRuleOption(section=sectionName, option ="clean", mandatory=True, type="bool")
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108 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
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109 iConfig = iConfigChecker.getConfig()
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110 self._setAttributesFromConfig(iConfig)
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111
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112 def _setAttributesFromConfig(self, iConfig):
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113 self.setProjectName(iConfig.get("project", "project_name"))
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114 sectionName = "classif_consensus"
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115 self.setDoClean(iConfig.get(sectionName, "clean"))
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116
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117 def setFastaFileName(self, fastaFileName):
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118 self._fastaFileName = fastaFileName
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119
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120 def setConfigFileName(self, configFileName):
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121 self._configFileName = configFileName
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122
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123 def setAddWickerCode(self, addWickerCode):
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124 self._addWickerCode = addWickerCode
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125
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126 def setReverseComp(self, reverseComp):
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127 self._reverseComp = reverseComp
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128
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129 def setDoClean(self, doClean):
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130 self._doClean = doClean
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131
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132 def setVerbosity(self, verbosity):
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133 self._verbosity = verbosity
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134
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135 def setProjectName(self, projectName):
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136 self._projectName = projectName
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137
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138 def _checkOptions(self):
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139 if self._fastaFileName == "":
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140 self._logAndRaise("ERROR: Missing input fasta file name")
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141
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142 def _logAndRaise(self, errorMsg):
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143 self._log.error(errorMsg)
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144 raise Exception(errorMsg)
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145
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146 def run(self):
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147 LoggerFactory.setLevel(self._log, self._verbosity)
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148 if self._configFileName:
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149 self._checkConfig()
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150 self._checkOptions()
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151 self._log.info("START TEclassifier PASTEC Edition")
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152 self._log.debug("Fasta file name: %s" % self._fastaFileName)
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153 nbSeq = FastaUtils.dbSize(self._fastaFileName)
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154 self._log.debug("Total number of sequences: %i)" % nbSeq)
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155
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156 #TODO: add step => avoid to re-launch DetectTEFeatures, if error with PASTEC (e.g. wrong bank format)
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157 #step 1
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158 iDF = DetectTEFeatures(self._fastaFileName, self._projectName, self._configFileName, self._doClean, self._verbosity)
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159 iDF.run()
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160
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161 #step 2
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162 iLP = LaunchPASTEC(configFileName = self._configFileName, inputFileName = self._fastaFileName, projectName = self._projectName, verbose = self._verbosity)
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163 iLP.run()
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164
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165 classifFileName = "%s.classif" % self._projectName
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166
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167 iSP = StatPastec(classifFileName)
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168 iSP.run()
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169
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170 if self._reverseComp:
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171 self._log.info("Reverse complement...")
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172 iRevComplAccording2Classif = ReverseComplementAccordingToClassif()
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173 iRevComplAccording2Classif.setFastaFile(self._fastaFileName)
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174 iRevComplAccording2Classif.setClassifFile(classifFileName)
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175 iRevComplAccording2Classif.run()
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176 tmpFastaFileName = "%s_negStrandReversed.fa" % os.path.splitext(self._fastaFileName)[0]
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177 else:
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178 tmpFastaFileName = self._fastaFileName
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179
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180 if self._addWickerCode:
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181 self._log.info("Rename headers according to Wicker's code...")
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182 iRHC = RenameHeaderClassif(classifFileName, tmpFastaFileName, self._projectName)
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183 iRHC.setOutputFileName("")
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184 iRHC.run()
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185 if self._doClean:
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186 os.remove(tmpFastaFileName)
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187
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188 self._log.info("END TEclassifier PASTEC Edition")
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189
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190 if __name__ == "__main__":
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191 iLaunch = TEclassifierPE()
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192 iLaunch.setAttributesFromCmdLine()
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193 iLaunch.run() |
