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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 import subprocess
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36
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37 LOG_DEPTH = "repet.tools"
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38
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39 ##Launch MATCHER
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40 #
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41 class LaunchMatcher(object):
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42
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43 def __init__(self, align="", queryFileName="", subjectFileName="", evalue="1e-10", doJoin=False, keepConflict=False, prefix="", doClean = False, verbosity = 0):
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44 self._alignFileName = align
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45 self._queryFileName = queryFileName
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46 self.setSubjectFileName(subjectFileName)
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47 self.setOutPrefix(prefix)
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48 self._doJoin = doJoin
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49 self._eValue = evalue
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50 self._keepConflict = keepConflict
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51
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52 self._doClean = doClean
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53 self._verbosity = verbosity
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54 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
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55
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56 def setAttributesFromCmdLine(self):
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57 description = "Launch Matcher."
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58 epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
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59 epilog += "\t$ python LaunchMatcher.py -a in.align -v 0"
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60 epilog += "\n\t"
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61 epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
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62 epilog += "\t$ python LaunchMatcher.py -a in.align -q query.fa -s nr.fa -c -v 2"
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63 parser = RepetOptionParser(description = description, epilog = epilog)
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64 parser.add_option("-a", "--align", dest = "align", action = "store", type = "string", help = "input align file name [compulsory] [format: align]", default = "")
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65 parser.add_option("-q", "--query", dest = "query", action = "store", type = "string", help = "query fasta file name [optional] [format: fasta]", default = "")
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66 parser.add_option("-s", "--subject", dest = "subject", action = "store", type = "string", help = "subject fasta file name [optional] [format: fasta]", default = "")
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67 parser.add_option("-e", "--evalue", dest = "evalue", action = "store", type = "string", help = "E-value filter [default: 1e-10]", default = "1e-10")
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68 parser.add_option("-j", "--join", dest = "doJoin", action = "store_true", help = "join matches [default: False]", default = False)
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69 parser.add_option("-k", "--keepConflict",dest = "keepConflict", action = "store_true", help = "keep conflicting subjects [default: False]", default = False)
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70 parser.add_option("-o", "--outPrefix", dest = "outPrefix", action = "store", type = "string", help = "output file prefix [default: align file name]", default = "")
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71 parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [default: False]", default = False)
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72 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [default: 1]", default = 1)
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73 options = parser.parse_args()[0]
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74 self._setAttributesFromOptions(options)
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75
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76 def _setAttributesFromOptions(self, options):
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77 self.setAlignFileName(options.align)
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78 self.setQueryFileName(options.query)
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79 self.setSubjectFileName(options.subject)
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80 self.setEvalue(options.evalue)
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81 self.setDoJoin(options.doJoin)
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82 self.setKeepConflicts(options.keepConflict)
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83 self.setOutPrefix(options.outPrefix)
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84 self.setDoClean(options.doClean)
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85 self.setVerbosity(options.verbosity)
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86
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87 def setAlignFileName(self, alignFileName):
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88 self._alignFileName = alignFileName
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89
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90 def setQueryFileName(self, queryFileName):
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91 self._queryFileName = queryFileName
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92
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93 def setSubjectFileName(self, subjectFileName):
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94 self._subjectFileName = subjectFileName
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95
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96 def setEvalue(self, evalue):
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97 self._eValue = evalue
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98
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99 def setDoJoin(self, doJoin):
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100 self._doJoin = doJoin
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101
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102 def setKeepConflicts(self, keepConflict):
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103 self._keepConflict = keepConflict
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104
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105 def setOutPrefix(self, outPrefix):
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106 if outPrefix == "":
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107 self._outPrefix = self._alignFileName
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108 else:
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109 self._outPrefix = outPrefix
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110
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111 def setDoClean(self, doClean):
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112 self._doClean = doClean
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113
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114 def setVerbosity(self, verbosity):
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115 self._verbosity = verbosity
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116
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117 def _checkOptions(self):
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118 if self._alignFileName == "":
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119 self._logAndRaise("ERROR: Missing input align file name")
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120
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121 def _logAndRaise(self, errorMsg):
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122 self._log.error(errorMsg)
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123 raise Exception(errorMsg)
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124
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125 def _getMatcherCmd(self):
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126 lArgs = []
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127 lArgs.append("-m %s" % self._alignFileName)
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128 if self._queryFileName:
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129 lArgs.append("-q %s" % self._queryFileName)
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130 if self._subjectFileName:
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131 lArgs.append("-s %s" % self._subjectFileName)
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132 if self._doJoin:
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133 lArgs.append("-j")
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134 lArgs.append("-E %s" % self._eValue)
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135 lArgs.append("-B %s" % self._outPrefix)
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136 if self._keepConflict:
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137 lArgs.append("-a")
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138 lArgs.append("-v %i" % (self._verbosity - 1))
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139 return self._getSystemCommand("matcher", lArgs)
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140
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141 def _getSystemCommand(self, prg, lArgs):
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142 systemCmd = prg
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143 for arg in lArgs:
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144 systemCmd += " " + arg
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145 return systemCmd
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146
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147 def run(self):
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148 LoggerFactory.setLevel(self._log, self._verbosity)
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149 self._checkOptions()
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150 self._log.info("START LaunchMatcher")
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151 self._log.debug("Align file name: %s" % self._alignFileName)
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152 self._log.debug("Query file name: %s" % self._queryFileName)
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153 self._log.debug("Subject file name: %s" % self._subjectFileName)
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154 #TODO: clean files
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155 # if self._doClean:
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156 # self._log.warning("Files will be cleaned")
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157 cmd = self._getMatcherCmd()
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158 process = subprocess.Popen(cmd, shell = True)
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159 self._log.debug("Running : %s" % cmd)
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160 process.communicate()
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161 if process.returncode != 0:
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162 self._logAndRaise("ERROR when launching '%s'" % cmd)
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163 self._log.info("END LaunchMatcher")
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164
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165 if __name__ == "__main__":
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166 iLaunch = LaunchMatcher()
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167 iLaunch.setAttributesFromCmdLine()
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168 iLaunch.run() |
