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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 MafftProgramLauncher on several files in parallel on a cluster.
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5
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6
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7 from pyRepet.launcher.AbstractClusterLauncher import *
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8 from commons.launcher.MafftProgramLauncher import MafftProgramLauncher
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9
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10
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11 class MafftClusterLauncher( AbstractClusterLauncher ):
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12 """
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13 Launch Mafft on several files in parallel on a cluster.
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14 """
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15
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16 def __init__( self ):
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17 """
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18 Constructor.
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19 """
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20 AbstractClusterLauncher.__init__( self )
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21 AbstractClusterLauncher.setAcronym( self, "Mafft" )
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22
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23 self._cmdLineSpecificOptions = "p:"
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24
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25 self._exeWrapper = "MafftProgramLauncher.py"
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26 self._prgLauncher = None
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27 self._prgLauncher = self.getProgramLauncherInstance()
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28
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29
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30 def getSpecificHelpAsString( self ):
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31 """
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32 Return the specific help as a string.
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33 """
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34 string = ""
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35 string += "\nspecific options:"
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36 string += "\n -p: parameters for 'mafft' (default='--auto')"
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37 return string
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38
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39
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40 def getProgramParameters( self ):
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41 return self._prgLauncher.getProgramParameters()
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42
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43
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44 def getProgramLauncherInstance( self ):
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45 if self._prgLauncher == None:
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46 self._prgLauncher = MafftProgramLauncher()
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47 self._prgLauncher.setInputFile( GENERIC_IN_FILE )
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48 self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) )
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49 self._prgLauncher.setClean()
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50 self._prgLauncher.setVerbosityLevel( 1 )
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51 self._prgLauncher.setListFilesToKeep()
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52 self._prgLauncher.setListFilesToRemove()
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53 return self._prgLauncher
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54
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55
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56 if __name__ == "__main__":
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57 i = MafftClusterLauncher()
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58 i.setAttributesFromCmdLine()
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59 i.run()
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