diff commons/launcher/MafftClusterLauncher.py @ 18:94ab73e8a190

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/MafftClusterLauncher.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,59 @@
+#!/usr/bin/env python
+
+##@file
+# Launch MafftProgramLauncher on several files in parallel on a cluster.
+
+
+from pyRepet.launcher.AbstractClusterLauncher import *
+from commons.launcher.MafftProgramLauncher import MafftProgramLauncher
+
+
+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
+    
+    
+if __name__ == "__main__":
+    i = MafftClusterLauncher()
+    i.setAttributesFromCmdLine()
+    i.run()