def getProgramLauncherInstance( self ): if self._prgLauncher == None: self._prgLauncher = MafftProgramLauncher() self._prgLauncher.setInputFile( GENERIC_IN_FILE ) self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) ) self._prgLauncher.setClean() self._prgLauncher.setVerbosityLevel( 1 ) self._prgLauncher.setListFilesToKeep() self._prgLauncher.setListFilesToRemove() return self._prgLauncher
class MafftClusterLauncher( AbstractClusterLauncher ): """ Launch Mafft on several files in parallel on a cluster. """ def __init__( self ): """ Constructor. """ AbstractClusterLauncher.__init__( self ) AbstractClusterLauncher.setAcronym( self, "Mafft" ) self._cmdLineSpecificOptions = "p:" self._exeWrapper = "MafftProgramLauncher.py" self._prgLauncher = None self._prgLauncher = self.getProgramLauncherInstance() def getSpecificHelpAsString( self ): """ Return the specific help as a string. """ string = "" string += "\nspecific options:" string += "\n -p: parameters for 'mafft' (default='--auto')" return string def getProgramParameters( self ): return self._prgLauncher.getProgramParameters() def getProgramLauncherInstance( self ): if self._prgLauncher == None: self._prgLauncher = MafftProgramLauncher() self._prgLauncher.setInputFile( GENERIC_IN_FILE ) self._prgLauncher.setOutputFile( "%s.fa_aln" % ( GENERIC_IN_FILE ) ) self._prgLauncher.setClean() self._prgLauncher.setVerbosityLevel( 1 ) self._prgLauncher.setListFilesToKeep() self._prgLauncher.setListFilesToRemove() return self._prgLauncher