diff commons/launcher/MapClusterLauncher.py @ 31:0ab839023fe4

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/MapClusterLauncher.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+
+##@file
+# Launch MapProgramLauncher.py on several files in parallel on a cluster.
+
+
+import os
+import sys
+import getopt
+import exceptions
+
+from pyRepet.launcher.AbstractClusterLauncher import *
+from commons.launcher.MapProgramLauncher import MapProgramLauncher
+
+
+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 ) )
+            #TESt de SATannot verifier si clean est a vrai
+            #self._prgLauncher.setClean()
+            self._prgLauncher.setVerbosityLevel( 1 )
+            self._prgLauncher.setListFilesToKeep()
+            self._prgLauncher.setListFilesToRemove()
+        return self._prgLauncher
+    
+    
+if __name__ == "__main__":
+    i = MapClusterLauncher()
+    i.setAttributesFromCmdLine()
+    i.run()