--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/MapProgramLauncher.py	Tue Apr 30 14:33:21 2013 -0400
@@ -0,0 +1,251 @@
+#!/usr/bin/env python
+
+##@file
+# Launch Map (multiple alignment).
+#
+# options:
+#      -h: this help
+#      -i: name of the input file (format='fasta')
+#      -s: size above which a gap is not penalized anymore (default='50')
+#      -m: penalty for a mismatch (default='-8')
+#      -O: penalty for a gap opening (default='16')
+#      -e: penalty for a gap extension (default='4')
+#      -o: name of the output file (format='aligned fasta', default=inFile+'.fa_aln')
+#      -c: clean
+#      -v: verbosity level (default=0/1)
+
+
+import sys
+import os
+
+from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
+from commons.core.seq.FastaUtils import FastaUtils
+from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
+from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
+
+
+class MapProgramLauncher( AbstractProgramLauncher ):
+    """
+    Launch Map (multiple alignment).
+    """
+    
+    
+    def __init__( self ):
+        """
+        Constructor.
+        """
+        AbstractProgramLauncher.__init__( self )
+        self._prgName = "rpt_map"
+        self._formatInFile = "fasta"
+        self._cmdLineSpecificOptions = "s:m:O:e:o:"
+        self._gapSize = 50
+        self._mismatchPenalty = -8
+        self._gapOpenPenalty = 16
+        self._gapExtendPenalty = 4
+        self._outFile = ""
+        
+    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', match=10)" % ( self.getMismatchPenalty() )
+        string += "\n     -O: penalty for a gap opening (default='%i')" % ( self.getGapOpenPenalty() )
+        string += "\n     -e: penalty for a gap extension (default='%i')" % ( self.getGapExtendPenalty() )
+        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 == "-s":
+            self.setGapSize( a )
+        elif o == "-m":
+            self.setMismatchPenalty( a )
+        elif o == "-O":
+            self.setGapOpenPenalty( a )
+        elif o == "-e":
+            self.setGapExtendPenalty( a )
+        elif o == "-o":
+            self.setOutputFile( a )
+
+                        
+    def setGapSize( self, arg ):
+        self._gapSize = int(arg)
+        
+        
+    def setMismatchPenalty( self, arg ):
+        self._mismatchPenalty = int(arg)
+        
+        
+    def setGapOpenPenalty( self, arg ):
+        self._gapOpenPenalty = int(arg)
+        
+        
+    def setGapExtendPenalty( self, arg ):
+        self._gapExtendPenalty = int(arg)
+        
+        
+    def getGapSize( self ):
+        return self._gapSize
+        
+        
+    def getMismatchPenalty( self ):
+        return self._mismatchPenalty
+        
+        
+    def getGapOpenPenalty( self ):
+        return self._gapOpenPenalty
+        
+        
+    def getGapExtendPenalty( self ):
+        return self._gapExtendPenalty
+        
+        
+    def checkSpecificAttributes( self ):
+        """
+        Check the specific attributes before running the program.
+        """
+        if self.getGapSize() <= 0:
+            string = "ERROR: gap size should be > 0"
+            print string
+            print self.getHelpAsString()
+            sys.exit(1)
+        if self.getMismatchPenalty() >= 0:
+            string = "ERROR: mismatch penalty should be < 0"
+            print string
+            print self.getHelpAsString()
+            sys.exit(1)
+        if self.getGapOpenPenalty() < 0:
+            string = "ERROR: gap opening penalty should be >= 0"
+            print string
+            print self.getHelpAsString()
+            sys.exit(1)
+        if self.getGapExtendPenalty() < 0:
+            string = "ERROR: gap extension penalty should be >= 0"
+            print string
+            print self.getHelpAsString()
+            sys.exit(1)
+        if self.getOutputFile() == "":
+            self.setOutputFile( "%s.fa_aln" % ( self.getInputFile() ) )
+            
+            
+    def setWrapperCommandLine( self ):
+        """
+        Set the command-line of the wrapper.
+        Required for MapClusterLauncher.
+        """
+        self._wrpCmdLine = self.getWrapperName()
+        self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
+        self._wrpCmdLine += " -s %i" % ( self.getGapSize() )
+        self._wrpCmdLine += " -m %i" % ( self.getMismatchPenalty() )
+        self._wrpCmdLine += " -O %i" % ( self.getGapOpenPenalty() )
+        self._wrpCmdLine += " -e %i" % ( self.getGapExtendPenalty() )
+        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.shortH" % ( self.getInputFile() )
+        self._prgCmdLine += " %i" % ( self.getGapSize() )
+        self._prgCmdLine += " %i" % ( self.getMismatchPenalty() )
+        self._prgCmdLine += " %i" % ( self.getGapOpenPenalty() )
+        self._prgCmdLine += " %i" % ( self.getGapExtendPenalty() )
+        self._prgCmdLine += " > %s.shortH.fa_aln" % ( self.getInputFile() )
+        
+        
+    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 += "\ngap size: %i" % ( self.getGapSize() )
+        self._summary += "\nmismatch penalty: %i" % ( self.getMismatchPenalty() )
+        self._summary += "\ngap openning penalty: %i" % ( self.getGapOpenPenalty() )
+        self._summary += "\ngap extension penalty: %i" % ( self.getGapExtendPenalty() )
+        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()
+        
+        self.setProgramCommandLine()
+        cmd = self.getProgramCommandLine()
+        if self.getVerbosityLevel() > 0:
+            print "LAUNCH: %s" % ( cmd )
+            sys.stdout.flush()
+        returnStatus = os.system( cmd )
+        if returnStatus != 0:
+            string = "ERROR: program '%s' returned status '%i'" % ( self.getProgramName(), returnStatus )
+            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()
+        if self.getClean():
+            os.remove( "%s.shortH.fa_aln.initH" % ( self.getInputFile() ) )
+        
+        self.end()
+        
+        
+if __name__ == "__main__":
+    i = MapProgramLauncher()
+    i.setAttributesFromCmdLine()
+    i.run()