--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/MafftProgramLauncher.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,188 @@
+#!/usr/bin/env python
+
+##@file
+# Launch Mafft (multiple alignment).
+#
+# options:
+#      -h: this help
+#      -i: name of the input file (format='fasta')
+#      -p: parameters for 'mafft' (default='--auto')
+#      -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')
+#      -c: clean
+#      -v: verbosity level (default=0/1)
+
+
+import os
+import sys
+import getopt
+import exceptions
+
+from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
+from pyRepet.seq.fastaDB import *
+from commons.core.seq.FastaUtils import FastaUtils
+from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
+from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
+
+
+class MafftProgramLauncher( AbstractProgramLauncher ):
+    """
+    Launch Mafft (multiple alignment).
+    """
+    
+    
+    def __init__( self ):
+        """
+        Constructor.
+        """
+        AbstractProgramLauncher.__init__( self )
+        self._prgName = "mafft"
+        self._formatInFile = "fasta"
+        self._prgParam = "--auto"
+        self._cmdLineSpecificOptions = "p:o:"
+        
+        
+    def getSpecificHelpAsString( self ):
+        """
+        Return the specific help as a string.
+        """
+        string = ""
+        string += "\nspecific options:"
+        string += "\n     -p: parameters for '%s' (default='--auto')" % ( self.getProgramName() )
+        string += "\n     -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')"
+        return string
+    
+    
+    def setASpecificAttributeFromCmdLine( self, o, a="" ):
+        """
+        Set a specific attribute from the command-line arguments.
+        """
+        if o == "-p":
+            self.setProgramParameters( a )
+        elif o == "-o":
+            self.setOutputFile( a )
+            
+            
+    def checkSpecificAttributes( self ):
+        """
+        Check the specific attributes before running the program.
+        """
+        if self.getOutputFile() == "":
+            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
+            
+            
+    def setWrapperCommandLine( self ):
+        """
+        Set the command-line of the wrapper.
+        Required for MafftClusterLauncher.
+        """
+        self._wrpCmdLine = self.getWrapperName()
+        self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
+        self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() )
+        if self.getOutputFile() == "":
+            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
+        self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
+        if self.getClean():
+            self._wrpCmdLine += " -c"
+        self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
+        
+        
+    def setProgramCommandLine( self ):
+        """
+        Set the command-line of the program.
+        """
+        self._prgCmdLine = self.getProgramName()
+        self._prgCmdLine += " %s" % ( self.getProgramParameters() )
+        if self.getVerbosityLevel() == 0 and "--quiet" not in self._prgCmdLine:
+            self._prgCmdLine += " --quiet"
+        self._prgCmdLine += " %s.shortH" % ( self.getInputFile() )
+        self._prgCmdLine += " > %s.shortH.fa_aln" % ( self.getInputFile() )
+        if self._verbose < 2:
+            self._prgCmdLine += " 2> /dev/null"
+            
+            
+    def setListFilesToKeep( self ):
+        """
+        Set the list of files to keep.
+        """
+        if self.getOutputFile() == "":
+            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
+        self.appendFileToKeep( self.getOutputFile() )
+        
+        
+    def setListFilesToRemove( self ):
+        """
+        Set the list of files to remove.
+        """
+        self.appendFileToRemove( "%s.shortH" % ( self.getInputFile() ) )
+        self.appendFileToRemove( "%s.shortH.fa_aln" % ( self.getInputFile() ) )
+        self.appendFileToRemove( "%s.shortHlink" % ( self.getInputFile() ) )
+        
+        
+    def setSummary( self ):
+        self._summary = "input file: %s" % ( self.getInputFile() )
+        self._summary += "\nparameters: %s" % ( self.getProgramParameters() )
+        if self.getOutputFile() == "":
+            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
+        self._summary += "\noutput file: %s" % ( self.getOutputFile() )
+        
+        
+    def run( self ):
+        """
+        Run the program.
+        """
+        self.start()
+        
+        lInitHeaders = FastaUtils.dbHeaders( self.getInputFile(), self.getVerbosityLevel()-1 )
+        
+        csh = ChangeSequenceHeaders()
+        csh.setInputFile( self.getInputFile() )
+        csh.setFormat( "fasta" )
+        csh.setStep( 1 )
+        csh.setPrefix( "seq" )
+        csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) )
+        csh.setOutputFile( "%s.shortH" % ( self.getInputFile() ) )
+        csh.setVerbosityLevel( self.getVerbosityLevel() - 1 )
+        csh.run()
+        
+        bsDB = BioseqDB( "%s.shortH" % ( self.getInputFile() ) )
+        bsDB.upCase()
+        bsDB.save( "%s.shortHtmp" % ( self.getInputFile() ) )
+        del bsDB
+        os.rename( "%s.shortHtmp" % ( self.getInputFile() ),
+                   "%s.shortH" % ( self.getInputFile() ) )
+        
+        self.setProgramCommandLine()
+        cmd = self.getProgramCommandLine()
+        if self.getVerbosityLevel() > 0:
+            print "LAUNCH: %s" % ( cmd )
+            sys.stdout.flush()
+        exitStatus = os.system( cmd )
+        if exitStatus != 0:
+            string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
+            print string
+            sys.exit(1)
+            
+        csh.setInputFile( "%s.shortH.fa_aln" % ( self.getInputFile() ) )
+        csh.setFormat( "fasta" )
+        csh.setStep( 2 )
+        csh.setLinkFile( "%s.shortHlink" % ( self.getInputFile() ) )
+        csh.setOutputFile( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
+        csh.setVerbosityLevel( self.getVerbosityLevel() - 1 )
+        csh.run()
+        
+        absDB = AlignedBioseqDB( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
+        outFileHandler = open( self.getOutputFile(), "w" )
+        for header in lInitHeaders:
+            bs = absDB.fetch( header )
+            bs.upCase()
+            bs.write( outFileHandler )
+        outFileHandler.close()
+        os.remove( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
+        
+        self.end()
+        
+        
+if __name__ == "__main__":
+    i = MafftProgramLauncher()
+    i.setAttributesFromCmdLine()
+    i.run()