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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 from commons.core.LoggerFactory import LoggerFactory
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34 from commons.core.utils.RepetOptionParser import RepetOptionParser
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35 from commons.core.checker.ConfigChecker import ConfigRules
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36 from commons.core.checker.ConfigChecker import ConfigChecker
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37 import subprocess
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38 import glob
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39 import os
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40
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41 LOG_DEPTH = "repet.launchers"
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42
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43 class LaunchTRF(object):
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44
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45 def __init__(self, inFileName = "", outFileName = "", maxPeriod=15, doClean = False, verbosity = 0):
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46 self.inFileName = inFileName
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47 self.setOutFileName(outFileName)
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48 self.maxPeriod=maxPeriod
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49 self._doClean = doClean
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50 self._verbosity = verbosity
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51 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
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52
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53 def setAttributesFromCmdLine(self):
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54 description = "Launch TRF to detect micro-satellites in sequences."
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55 epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
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56 epilog += "\t$ python LaunchTemplate.py -i file.fa -v 0"
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57 epilog += "\n\t"
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58 parser = RepetOptionParser(description = description, epilog = epilog)
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59 parser.add_option("-i", "--in", dest = "inFileName", action = "store", type = "string", help = "input file name [compulsory] [format: fasta]", default = "")
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60 parser.add_option("-o", "--out", dest = "outFileName", action = "store", type = "string", help = "output file name [default: <input>.TRF.set]", default = "")
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61 parser.add_option("-m", "--maxPeriod", dest = "maxPeriod", action = "store", type = "int", help = " maximum period size to report [default: 15]", default = 15)
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62 parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False)
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63 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1)
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64 options = parser.parse_args()[0]
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65 self._setAttributesFromOptions(options)
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66
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67 def _setAttributesFromOptions(self, options):
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68 self.setInFileName(options.inFileName)
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69 self.setOutFileName(options.outFileName)
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70 self.maxPeriod = options.maxPeriod
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71 self.setDoClean(options.doClean)
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72 self.setVerbosity(options.verbosity)
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73
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74 def setInFileName(self, inFileName):
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75 self.inFileName = inFileName
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76
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77 def setOutFileName(self, outFileName):
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78 if outFileName == "":
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79 self._outFileName = "%s.TRF.set" % self.inFileName
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80 else:
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81 self._outFileName = outFileName
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82
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83 def setDoClean(self, doClean):
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84 self._doClean = doClean
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85
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86 def setVerbosity(self, verbosity):
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87 self._verbosity = verbosity
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88
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89 def _checkOptions(self):
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90 if self.inFileName == "":
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91 self._logAndRaise("ERROR: Missing input file name")
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92
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93 def _logAndRaise(self, errorMsg):
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94 self._log.error(errorMsg)
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95 raise Exception(errorMsg)
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96
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97
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98 def _launchTRF(self):
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99 cmd = "trf %s 2 3 5 80 10 20 %d -h -d" % (self.inFileName, self.maxPeriod)
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100 self._log.debug("Running : %s" % cmd)
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101 process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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102 output = process.communicate()
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103 self._log.debug("Output:\n%s" % output[0])
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104
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105 def _parseTRF(self):
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106 self._log.debug("Parsing TRF output")
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107 with open( "%s.2.3.5.80.10.20.%d.dat" % (self.inFileName, self.maxPeriod),'r') as inFile:
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108 with open(self._outFileName,'w') as outFile:
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109 nbPatterns = 0
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110 nbInSeq = 0
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111 for line in inFile.readlines():
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112 if line == "":
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113 break
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114 data = line.split(" ")
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115 if len(data) > 1 and "Sequence:" in data[0]:
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116 nbInSeq += 1
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117 seqName = data[1][:-1]
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118 if len(data) < 14:
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119 continue
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120 nbPatterns += 1
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121 consensus = data[13]
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122 copyNb = int( float(data[3]) + 0.5 )
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123 start = data[0]
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124 end = data[1]
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125 outFile.write( "%i\t(%s)%i\t%s\t%s\t%s\n" % ( nbPatterns, consensus, copyNb, seqName, start, end ) )
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126 self._log.debug("Finished Parsing TRF output")
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127
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128 def _clean(self):
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129 try:
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130 os.remove("%s.2.3.5.80.10.20.%d.dat" % (self.inFileName, self.maxPeriod))
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131 except:pass
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132
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133
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134 def run(self):
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135 """
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136 Launch TRF to detect micro-satellites in sequences.
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137 """
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138 LoggerFactory.setLevel(self._log, self._verbosity)
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139 self._checkOptions()
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140 self._log.info("START Launch")
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141 self._log.debug("Input file name: %s" % self.inFileName)
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142
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143 self._launchTRF()
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144 self._parseTRF()
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145
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146 if self._doClean:
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147 self._log.warning("Files will be cleaned")
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148 self._clean()
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149 self._log.info("END Launch")
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150
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151 if __name__ == "__main__":
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152 iLaunchTRF = LaunchTRF()
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153 iLaunchTRF.setAttributesFromCmdLine()
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154 iLaunchTRF.run()
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155
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