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1 #!/usr/bin/env python
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2
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3 ##@file
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4 # Launch Blat (pairwise alignment).
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5 #
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6 # options:
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7 # -h: this help
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8 # -i: name of the input file (queries, format='fasta')
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9 # -s: name of the subject file (format='fasta')
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10 # -p: parameters for 'blat' (default='-d 2')
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11 # -o: name of the output file (format='align', default=inFile+'.align')
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12 # -c: clean
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13 # -v: verbosity level (default=0/1)
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14
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15
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16 import os
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17 import sys
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18
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19 from commons.pyRepetUnit.components.AbstractProgramLauncher import AbstractProgramLauncher
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20
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21
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22 class BlatProgramLauncher( AbstractProgramLauncher ):
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23 """
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24 Launch Blat (pairwise alignment).
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25 """
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26
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27 def __init__( self ):
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28 """
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29 Constructor.
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30 """
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31 AbstractProgramLauncher.__init__( self )
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32 self._prgName = "blat"
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33 self._formatInFile = "fasta"
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34 self._sbjFile = ""
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35 self._prgParam = ""
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36 self._allByAll = False
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37
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38
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39 def getHelpAsString( self ):
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40 string = AbstractProgramLauncher.getHelpAsString(self)
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41 string += "\nspecific options:"
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42 string += "\n -s: name of the subject file (database, format='fasta')"
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43 string += "\n -p: parameters for '%s'" % ( self.getProgramName() )
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44 string += "\n -A: same sequences (all-by-all)"
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45 string += "\n -o: name of the output file (format='align', default=inFile+'.align')"
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46 return string
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47
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48 def getCmdLineOptions(self):
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49 return AbstractProgramLauncher.getCmdLineOptions(self) + "s:p:Ao:"
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50
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51 def setAttributesFromCmdLine( self, o, a = "" ):
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52 AbstractProgramLauncher.setAttributesFromCmdLine(self, o, a)
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53 if o == "-s":
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54 self.setSubjectFile( a )
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55 elif o == "-p":
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56 self.setProgramParameters( a )
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57 elif o == "-A":
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58 self.setAllByAll()
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59 elif o == "-o":
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60 self.setOutputFile( a )
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61
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62
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63 def setSubjectFile( self, arg ):
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64 self._sbjFile = arg
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65
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66
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67 def getSubjectFile( self ):
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68 return self._sbjFile
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69
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70
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71 def setAllByAll( self ):
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72 self._allByAll = True
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73
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74
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75 def getAllByAll( self ):
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76 return self._allByAll
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77
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78
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79 def check( self ):
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80 """
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81 Check the specific attributes before running the program.
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82 """
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83 AbstractProgramLauncher.check(self)
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84 if self._sbjFile == "":
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85 string = "ERROR: missing subject file (-s)"
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86 print string
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87 print self.getHelpAsString()
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88 sys.exit(1)
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89 if self.getOutputFile() == "":
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90 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
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91
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92
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93 def setWrapperCommandLine( self ):
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94 """
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95 Set the command-line of the wrapper.
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96 Required for BlatClusterLauncher.
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97 """
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98 self._wrpCmdLine = self.getWrapperName()
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99 self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
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100 self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() )
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101 if self.getProgramParameters() != "":
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102 self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() )
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103 if self.getAllByAll():
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104 self._wrpCmdLine += " -A"
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105 if self.getOutputFile() == "":
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106 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
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107 self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
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108 if self.getClean():
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109 self._wrpCmdLine += " -c"
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110 self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
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111
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112
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113 def setProgramCommandLine( self ):
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114 """
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115 Set the command-line of the program.
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116 """
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117 self._prgCmdLine = self.getProgramName()
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118 self._prgCmdLine += " %s" % ( self.getSubjectFile() )
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119 self._prgCmdLine += " %s" % ( self.getInputFile() )
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120 if self.getProgramParameters() != "":
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121 self._prgCmdLine += " %s" % ( self.getProgramParameters() )
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122 self._prgCmdLine += " -out=blast8"
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123 self._prgCmdLine += " %s.blast" % ( self.getInputFile() )
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124
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125
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126 def setListFilesToKeep( self ):
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127 """
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128 Set the list of files to keep.
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129 """
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130 if self.getOutputFile() == "":
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131 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
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132 self.appendFileToKeep( self.getOutputFile() )
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133
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134
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135 def setListFilesToRemove( self ):
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136 """
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137 Set the list of files to remove.
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138 """
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139 self.appendFileToRemove( "%s.blast" % ( self.getInputFile() ) )
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140
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141
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142 def convertBlastIntoAlign( self ):
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143 """
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144 Convert a 'blast' file into the 'align' format.
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145 """
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146 cmd = os.environ["REPET_PATH"] + "/bin/blast2align.py"
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147 cmd += " -i %s.blast" % ( self.getInputFile() )
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148 cmd += " -o %s" % ( self.getOutputFile() )
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149 exitStatus = os.system( cmd )
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150 if exitStatus != 0:
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151 string = "ERROR while converting 'blast' file into 'align' format"
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152 print string
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153 sys.exit(1)
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154
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155
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156 def setSummary( self ):
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157 self._summary = "input file: %s" % ( self.getInputFile() )
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158 self._summary += "\nsubject file: %s" % ( self.getSubjectFile() )
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159 self._summary += "\nparameters: %s" % ( self.getProgramParameters() )
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160 if self.getAllByAll():
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161 self._summary += "\nall-by-all"
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162 if self.getOutputFile() == "":
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163 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
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164 self._summary += "\noutput file: %s" % ( self.getOutputFile() )
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165
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166
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167 def run( self ):
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168 """
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169 Run the program.
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170 """
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171 self.start()
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172
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173 self.setProgramCommandLine()
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174 cmd = self.getProgramCommandLine()
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175 if self.getVerbosityLevel() > 0:
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176 print "LAUNCH: %s" % ( cmd )
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177 sys.stdout.flush()
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178 exitStatus = os.system( cmd )
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179 if exitStatus != 0:
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180 string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
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181 print string
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182 sys.exit(1)
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183
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184 self.convertBlastIntoAlign()
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185
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186 self.end()
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187
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188
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189 if __name__ == "__main__":
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190 i = BlatProgramLauncher()
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191 i.checkAttributesFromCmdLine()
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192 i.run()
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