def getProgramLauncherInstance( self ): if self._prgLauncher == None: self._prgLauncher = MapProgramLauncher() 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 MapClusterLauncher( AbstractClusterLauncher ): """ Launch Map on several files in parallel on a cluster. """ def __init__( self ): """ Constructor. """ AbstractClusterLauncher.__init__( self ) AbstractClusterLauncher.setAcronym( self, "Map" ) self._cmdLineSpecificOptions = "s:m:O:e:" self._exeWrapper = "MapProgramLauncher.py" self._prgLauncher = None self._prgLauncher = self.getProgramLauncherInstance() def getSpecificHelpAsString( self ): """ Return the specific help as a string. """ string = "" string += "\nspecific options:" string += "\n -s: size above which a gap is not penalized anymore (default='%i')" % ( self.getGapSize() ) string += "\n -m: penalty for a mismatch (default='%i')" % ( self.getMismatchPenalty() ) string += "\n -O: penalty for a gap openning (default='%i')" % ( self.getGapOpenPenalty() ) string += "\n -e: penalty for a gap extension (default='%i')" % ( self.getGapExtendPenalty() ) return string def getGapSize( self ): return self._prgLauncher.getGapSize() def getMismatchPenalty( self ): return self._prgLauncher.getMismatchPenalty() def getGapOpenPenalty( self ): return self._prgLauncher.getGapOpenPenalty() def getGapExtendPenalty( self ): return self._prgLauncher.getGapExtendPenalty() def getProgramLauncherInstance( self ): if self._prgLauncher == None: self._prgLauncher = MapProgramLauncher() 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