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