--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/launcher/NWalignProgramLauncher.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,187 @@
+#!/usr/bin/env python
+
+##@file
+# Launch NWalign (pairwise alignment).
+#
+# options:
+#      -h: this help
+#      -i: name of the input file (queries, format='fasta')
+#      -s: name of the subject file (format='fasta')
+#      -p: parameters for 'NWalign' (default='-d 2')
+#      -o: name of the output file (format='align', default=inFile+'.align')
+#      -c: clean
+#      -v: verbosity level (default=0/1)
+
+
+import os
+import sys
+
+from pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
+from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
+from commons.core.coord.AlignUtils import AlignUtils
+
+
+class NWalignProgramLauncher( AbstractProgramLauncher ):
+    """
+    Launch NWalign (pairwise alignment).
+    """
+    
+    def __init__( self ):
+        """
+        Constructor.
+        """
+        AbstractProgramLauncher.__init__( self )
+        self._prgName = "NWalign"
+        self._formatInFile = "fasta"
+        self._sbjFile = ""
+        self._prgParam = ""
+        self._cmdLineSpecificOptions = "s:p:o:"
+        
+        
+    def getSpecificHelpAsString( self ):
+        """
+        Return the specific help as a string.
+        """
+        string = ""
+        string += "\nspecific options:"
+        string += "\n     -s: name of the subject file (format='fasta')"
+        string += "\n     -p: parameters for '%s'" % ( self.getProgramName() )
+        string += "\n     -o: name of the output file (format='align', default=inFile+'.align')"
+        return string
+    
+    
+    def setASpecificAttributeFromCmdLine( self, o, a="" ):
+        """
+        Set a specific attribute from the command-line arguments.
+        """
+        if o =="-s":
+            self.setSubjectFile( a )
+        elif o == "-p":
+            self.setProgramParameters( a )
+        elif o == "-o":
+            self.setOutputFile( a )
+            
+            
+    def setSubjectFile( self, arg ):
+        self._sbjFile = arg
+        
+        
+    def getSubjectFile( self ):
+        return self._sbjFile
+    
+    
+    def checkSpecificAttributes( self ):
+        """
+        Check the specific attributes before running the program.
+        """
+        if self._sbjFile == "":
+            string = "ERROR: missing subject file (-s)"
+            print string
+            print self.getHelpAsString()
+            sys.exit(1)
+        if self.getOutputFile() == "":
+            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
+            
+            
+    def setWrapperCommandLine( self ):
+        """
+        Set the command-line of the wrapper.
+        Required for NWalignClusterLauncher.
+        """
+        self._wrpCmdLine = self.getWrapperName()
+        self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
+        self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() )
+        if self.getProgramParameters() != "":
+            self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() )
+        if self.getOutputFile() == "":
+            self.setOutputFile( "%s.align" % ( 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()
+        if self.getProgramParameters() != "":
+            self._prgCmdLine += " %s" % ( self.getProgramParameters() )
+        self._prgCmdLine += " -o %s.afa" % ( self.getInputFile() )
+        self._prgCmdLine += " -v %i" % ( self.getVerbosityLevel() )
+        self._prgCmdLine += " %s" % ( self.getSubjectFile() )
+        self._prgCmdLine += " %s" % ( self.getInputFile() )
+        
+        
+    def setListFilesToKeep( self ):
+        """
+        Set the list of files to keep.
+        """
+        if self.getOutputFile() == "":
+            self.setOutputFile( "%s.afa" % ( self.getInputFile() ) )
+        self.appendFileToKeep( self.getOutputFile() )
+        
+        
+    def postprocess( self ):
+        absDB = AlignedBioseqDB( "%s.afa" % ( self.getInputFile() ) )
+        lHeaders = absDB.getHeaderList()
+        queryHeader = lHeaders[0]
+        subjectHeader = lHeaders[1]
+        queryLength = absDB.fetch( queryHeader ).getLength()
+        subjectLength = absDB.fetch( subjectHeader ).getLength()
+        lAligns = absDB.getAlignList( queryHeader, subjectHeader )
+        for i in lAligns:
+            if "re-oriented" in i.getQueryName():
+                i.setQueryName( queryHeader.replace(" re-oriented","") )
+                start = i.getQueryStart()
+                end = i.getQueryEnd()
+                i.setQueryStart( queryLength - end + 1 )
+                i.setQueryEnd( queryLength - start + 1 )
+            if "re-oriented" in i.getSubjectName():
+                i.setSubjectName( subjectHeader.replace(" re-oriented","") )
+                start = i.getSubjectStart()
+                end = i.getSubjectEnd()
+                i.setSubjectEnd( subjectLength - end + 1 )
+                i.setSubjectStart( subjectLength - start + 1 )
+            if not i.isQueryOnDirectStrand():
+                i.reverse()
+        AlignUtils.writeListInFile( lAligns, self.getOutputFile() )
+        os.remove( "%s.afa" % ( self.getInputFile() ) )
+        
+        
+    def setSummary( self ):
+        self._summary = "input file: %s" % ( self.getInputFile() )
+        self._summary += "\nsubject file: %s" % ( self.getSubjectFile() )
+        self._summary += "\nparameters: %s" % ( self.getProgramParameters() )
+        if self.getOutputFile() == "":
+            self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
+        self._summary += "\noutput file: %s" % ( self.getOutputFile() )
+        
+        
+    def run( self ):
+        """
+        Run the program.
+        """
+        self.start()
+        
+        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)
+            
+        self.postprocess()
+        
+        self.end()
+        
+        
+if __name__ == "__main__":
+    i = NWalignProgramLauncher()
+    i.setAttributesFromCmdLine()
+    i.run()