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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 BLASTER
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40 #
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41 class LaunchBlaster(object):
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42
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43 def __init__(self, queryFileName = "", subjectFileName = "", evalue = 1e-300, identity = 90, length = 100, doAllByall = False, type = "ncbi", nbCPU = 1, program="blastn",extraParams="", doClean = False, verbosity = 0):
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44 self._queryFileName = queryFileName
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45 self.setSubjectFileName(subjectFileName)
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46 self._eValue = evalue
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47 self._identity = identity
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48 self._length = length
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49 self._doAllByall = doAllByall
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50 self._blastType = type
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51 self._program = program
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52 self._extraParams = extraParams
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53 self._nbCPU = nbCPU
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54 self._doClean = doClean
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55 self._verbosity = verbosity
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56 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
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57
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58 def setAttributesFromCmdLine(self):
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59 description = "Launch Blaster."
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60 epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
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61 epilog += "\t$ python LaunchBlaster.py -q query.fa -v 0"
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62 epilog += "\n\t"
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63 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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64 epilog += "\t$ python LaunchBlaster.py -q query.fa -s nr.fa -c -v 2"
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65 parser = RepetOptionParser(description = description, epilog = epilog)
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66 parser.add_option("-q", "--query", dest = "query", action = "store", type = "string", help = "query fasta file name [compulsory] [format: fasta]", default = "")
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67 parser.add_option("-s", "--subject", dest = "subject", action = "store", type = "string", help = "subject fasta file name [default: query] [format: fasta]", default = "")
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68 parser.add_option("-e", "--evalue", dest = "evalue", action = "store", type = "string", help = "Blast e-value [default: 1e-300]", default = "1e-300")
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69 parser.add_option("-d", "--id", dest = "identity", action = "store", type = "int", help = "Blast identity [default: 90]", default = 90)
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70 parser.add_option("-l", "--length", dest = "length", action = "store", type = "int", help = "Minimal hit length [default: 100]", default = 100)
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71 parser.add_option("-a", "--aba", dest = "doAllByall", action = "store_true", help = "all-by-all Blast [default: False]", default = False)
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72 parser.add_option("-t", "--type", dest = "type", action = "store", type = "string", help = "Blast type [ncbi, wu, blastplus] [default: ncbi]", default = "ncbi")
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73 parser.add_option("-u", "--program", dest = "program", action = "store", type = "string", help = "Blast program type [blastn, blastx, blastx] [default: blastn]", default = "blastn")
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74 parser.add_option("-x", "--extraParams",dest = "extraParams", action = "store", type = "string", help = "Additional blast program parameters[default: '']", default = "")
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75 parser.add_option("-n", "--ncpu", dest = "cpu", action = "store", type = "int", help = "Number of CPUs to use [default: 1]", default = 1)
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76 parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [default: False]", default = False)
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77 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [default: 1]", default = 1)
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78 options = parser.parse_args()[0]
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79 self._setAttributesFromOptions(options)
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80
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81 def _setAttributesFromOptions(self, options):
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82 self.setQueryFileName(options.query)
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83 self.setSubjectFileName(options.subject)
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84 self.setEvalue(options.evalue)
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85 self.setIdentity(options.identity)
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86 self.setLength(options.length)
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87 self.setDoAllByall(options.doAllByall)
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88 self.setType(options.type)
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89 self.setProgram(options.program)
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90 self.setExtraParams(options.extraParams)
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91 self.setCPU(options.cpu)
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92 self.setDoClean(options.doClean)
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93 self.setVerbosity(options.verbosity)
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94
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95
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96 def setQueryFileName(self, queryFileName):
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97 self._queryFileName = queryFileName
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98
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99 def setSubjectFileName(self, subjectFileName):
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100 if subjectFileName == "":
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101 self._subjectFileName = self._queryFileName
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102 else:
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103 self._subjectFileName = subjectFileName
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104
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105 def setEvalue(self, evalue):
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106 self._eValue = evalue
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107
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108 def setIdentity(self, identity):
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109 self._identity = identity
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110
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111 def setLength(self, length):
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112 self._length = length
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113
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114 def setDoAllByall(self, doAllByall):
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115 self._doAllByall = doAllByall
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116
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117 def setType(self, blastType):
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118 self._blastType = blastType
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119
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120 def setProgram(self, program):
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121 self._program = program
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122
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123 def setExtraParams(self, extraParams):
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124 self._extraParams = extraParams
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125
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126 def setCPU(self, cpu):
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127 self._nbCPU = cpu
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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 _checkOptions(self):
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136 if self._queryFileName == "":
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137 self._logAndRaise("ERROR: Missing input fasta file name")
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138
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139 lBlastType = ["ncbi", "wu", "blastplus"]
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140 if self._blastType.lower() not in lBlastType:
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141 self._logAndRaise("ERROR: unknown Blast type '%s' - correct values are %s" % (self._blastType, lBlastType))
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142
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143 def _logAndRaise(self, errorMsg):
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144 self._log.error(errorMsg)
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145 raise Exception(errorMsg)
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146
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147 def _getBlasterCmd(self):
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148 lArgs = []
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149 lArgs.append("-n %s" % self._program)
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150 lArgs.append("-q %s" % self._queryFileName)
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151 lArgs.append("-s %s" % self._subjectFileName)
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152 lArgs.append("-B %s" % self._queryFileName)
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153 if self._doAllByall:
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154 lArgs.append("-a")
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155 lArgs.append("-E %s" % self._eValue)
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156 lArgs.append("-L %s" % self._length)
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157 lArgs.append("-I %s" % self._identity)
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158 if self._blastType == "ncbi":
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159 lArgs.append("-N")
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160 lArgs.append("-p '-a %s %s'" % (self._nbCPU, self._extraParams))
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161 elif self._blastType == "wu":
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162 lArgs.append("-W")
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163 lArgs.append("-p '-cpus=%s %s'" % (self._nbCPU, self._extraParams))
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164 elif self._blastType == "blastplus":
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165 lArgs.append("-X")
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166 lArgs.append("-p '-num_threads %s %s'" % (self._nbCPU, self._extraParams))
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167 # TODO: check the check option at the beginning of step 2 to allow to launch megablast for blast and blast+
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168 # elif config.get(sectionName, "blast") == "mega":
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169 # lArgs.append("-N")
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170 # lArgs.append("-n megablast")
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171 # elif config.get(sectionName, "blast") == "megablastplus":
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172 # lArgs.append("-X")
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173 # lArgs.append("-n megablast")
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174 if self._doClean:
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175 lArgs.append("-c")
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176 lArgs.append("-v %i" % (self._verbosity - 1))
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177 return self._getSystemCommand("blaster", lArgs)
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178
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179 def _getSystemCommand(self, prg, lArgs):
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180 systemCmd = prg
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181 for arg in lArgs:
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182 systemCmd += " " + arg
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183 return systemCmd
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184
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185 def run(self):
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186 LoggerFactory.setLevel(self._log, self._verbosity)
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187 self._checkOptions()
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188 self._log.info("START LaunchBlaster")
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189 self._log.debug("Query file name: %s" % self._queryFileName)
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190 self._log.debug("Subject file name: %s" % self._subjectFileName)
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191 if self._doClean:
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192 self._log.warning("Files will be cleaned")
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193 cmd = self._getBlasterCmd()
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194 process = subprocess.Popen(cmd, shell = True)
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195 self._log.debug("Running : %s" % cmd)
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196 process.communicate()
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197 if process.returncode != 0:
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198 self._logAndRaise("ERROR when launching '%s'" % cmd)
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199 self._log.info("END LaunchBlaster")
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200
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201 if __name__ == "__main__":
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202 iLaunch = LaunchBlaster()
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203 iLaunch.setAttributesFromCmdLine()
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204 iLaunch.run() |
