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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 Yass (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 'yass' (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 pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
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20
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21
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22 class YassProgramLauncher( AbstractProgramLauncher ):
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23 """
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24 Launch Yass (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 = "yass"
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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 self._cmdLineSpecificOptions = "s:p:Ao:"
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38
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39
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40 def getSpecificHelpAsString( self ):
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41 """
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42 Return the specific help as a string.
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43 """
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44 string = ""
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45 string += "\nspecific options:"
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46 string += "\n -s: name of the subject file (format='fasta')"
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47 string += "\n -p: parameters for '%s'" % ( self.getProgramName() )
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48 string += "\n -A: same sequences (all-by-all)"
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49 string += "\n -o: name of the output file (format='align', default=inFile+'.align')"
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50 return string
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51
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52
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53 def setASpecificAttributeFromCmdLine( self, o, a="" ):
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54 """
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55 Set a specific attribute from the command-line arguments.
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56 """
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57 if o =="-s":
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58 self.setSubjectFile( a )
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59 elif o == "-p":
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60 self.setProgramParameters( a )
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61 elif o == "-A":
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62 self.setAllByAll()
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63 elif o == "-o":
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64 self.setOutputFile( a )
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65
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66
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67 def setSubjectFile( self, arg ):
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68 self._sbjFile = arg
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69
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70
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71 def getSubjectFile( self ):
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72 return self._sbjFile
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73
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74
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75 def setAllByAll( self ):
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76 self._allByAll = True
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77
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78
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79 def getAllByAll( self ):
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80 return self._allByAll
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81
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82
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83 def checkSpecificAttributes( self ):
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84 """
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85 Check the specific attributes before running the program.
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86 """
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87 if self._sbjFile == "":
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88 string = "ERROR: missing subject file (-s)"
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89 print string
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90 print self.getHelpAsString()
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91 sys.exit(1)
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92 if self.getOutputFile() == "":
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93 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
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94
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95
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96 def setWrapperCommandLine( self ):
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97 """
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98 Set the command-line of the wrapper.
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99 Required for YassClusterLauncher.
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100 """
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101 self._wrpCmdLine = self.getWrapperName()
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102 self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
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103 self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() )
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104 if self.getProgramParameters() != "":
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105 self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() )
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106 if self.getAllByAll():
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107 self._wrpCmdLine += " -A"
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108 if self.getOutputFile() == "":
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109 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
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110 self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
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111 if self.getClean():
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112 self._wrpCmdLine += " -c"
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113 self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
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114
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115
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116 def setProgramCommandLine( self ):
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117 """
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118 Set the command-line of the program.
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119 """
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120 self._prgCmdLine = self.getProgramName()
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121 self._prgCmdLine += " -d 2"
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122 if self.getProgramParameters() != "":
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123 self._prgCmdLine += " %s" % ( self.getProgramParameters() )
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124 self._prgCmdLine += " -o %s.blast" % ( self.getInputFile() )
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125 self._prgCmdLine += " %s" % ( self.getInputFile() )
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126 self._prgCmdLine += " %s" % ( self.getSubjectFile() )
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127
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128
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129 def setListFilesToKeep( self ):
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130 """
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131 Set the list of files to keep.
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132 """
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133 if self.getOutputFile() == "":
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134 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
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135 self.appendFileToKeep( self.getOutputFile() )
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136
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137
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138 def setListFilesToRemove( self ):
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139 """
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140 Set the list of files to remove.
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141 """
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142 pass
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143
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144
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145 def convertBlastIntoAlign( self ):
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146 """
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147 Convert a 'blast' file into the 'align' format.
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148 """
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149 cmd = os.environ["REPET_PATH"] + "/bin/blast2align.py"
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150 cmd += " -i %s.blast" % ( self.getInputFile() )
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151 cmd += " -o %s" % ( self.getOutputFile() )
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152 exitStatus = os.system( cmd )
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153 if exitStatus != 0:
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154 string = "ERROR while converting 'blast' file into 'align' format"
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155 print string
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156 sys.exit(1)
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157
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158
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159 def setSummary( self ):
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160 self._summary = "input file: %s" % ( self.getInputFile() )
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161 self._summary += "\nsubject file: %s" % ( self.getSubjectFile() )
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162 self._summary += "\nparameters: %s" % ( self.getProgramParameters() )
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163 if self.getAllByAll():
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164 self._summary += "\nall-by-all"
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165 if self.getOutputFile() == "":
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166 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
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167 self._summary += "\noutput file: %s" % ( self.getOutputFile() )
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168
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169
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170 def run( self ):
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171 """
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172 Run the program.
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173 """
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174 self.start()
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175
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176 self.setProgramCommandLine()
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177 cmd = self.getProgramCommandLine()
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178 if self.getVerbosityLevel() > 0:
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179 print "LAUNCH: %s" % ( cmd )
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180 sys.stdout.flush()
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181 exitStatus = os.system( cmd )
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182 if exitStatus != 0:
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183 string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
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184 print string
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185 sys.exit(1)
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186
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187 self.convertBlastIntoAlign()
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188
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189 self.end()
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190
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191
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192 if __name__ == "__main__":
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193 i = YassProgramLauncher()
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194 i.setAttributesFromCmdLine()
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195 i.run()
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