--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/RepeatMaskerClusterLauncher.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,77 @@
+#!/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()