#!/usr/bin/env python

##@file
# Launch RepeatMaskerProgramLauncher on several files in parallel on a cluster.


import os
import sys
import getopt
import exceptions

from pyRepet.launcher.AbstractClusterLauncher import *
from commons.launcher.RepeatMaskerProgramLauncher import RepeatMaskerProgramLauncher


class RepeatMaskerClusterLauncher( AbstractClusterLauncher ):
    """
    Launch RepeatMasker on several files in parallel on a cluster.
    """
    
    def __init__( self ):
        """
        Constructor.
        """
        AbstractClusterLauncher.__init__( self )
        AbstractClusterLauncher.setAcronym( self, "RM" )
        
        self._cmdLineSpecificOptions = "s:n:gbl"
        
        self._exeWrapper = "RepeatMaskerProgramLauncher.py"
        self._prgLauncher = RepeatMaskerProgramLauncher()
        self._prgLauncher.setInputFile( GENERIC_IN_FILE )
        self._prgLauncher.setOutputFile( GENERIC_IN_FILE )
        self._prgLauncher.setClean()
        self._prgLauncher.setVerbosityLevel( 1 )
        self._prgLauncher.setListFilesToKeep()
        self._prgLauncher.setListFilesToRemove()
        
        
    def getSpecificHelpAsString( self ):
        """
        Return the specific help as a string.
        """
        string = ""
        string += "\nspecific options:"
        string += "\n     -s: name of the subject file (repeats, format='fasta')"
        string += "\n     -n: nb of processors to use in parallel (default=1)"
        string += "\n     -g: calculate the GC content"
        string += "\n     -b: skip bacterial insertion element check"
        string += "\n     -l: mask low-complexity DNA or simple repeats"
        return string
    
    
    def getSubjectFile( self ):
        return self._prgLauncher.getSubjectFile()
    
    
    def getNbProcessors( self ):
        return self._prgLauncher.getNbProcessors()
    
    
    def getCalculateGCcontent( self ):
        return self._prgLauncher.getCalculateGCcontent()
    
    
    def getSkipBacterialIsCheck( self ):
        return self._prgLauncher.getSkipBacterialIsCheck()
    
    
    def getMaskSsr( self ):
        return self._prgLauncher.getMaskSsr()
    
    
if __name__ == "__main__":
    i = RepeatMaskerClusterLauncher()
    i.setAttributesFromCmdLine()
    i.run()