--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/tools/OrientSequences.py	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,375 @@
+#!/usr/bin/env python
+
+"""
+Interface to orient sequences before making a multiple alignment.
+Use hashing or suffix tree to get an idea of the appropriate strand.
+Use 'orienter' by default, otherwise use 'mummer'.
+"""
+
+import sys
+import os
+import glob
+import getopt
+
+from commons.core.seq.BioseqDB import BioseqDB
+import pyRepet.seq.fastaDB
+from commons.core.checker.CheckerUtils import CheckerUtils
+
+class OrientSequences( object ):
+    """
+    Interface to orient sequences before making a multiple alignment.
+    Use hashing or suffix tree to get an idea of the appropriate strand.
+    Use 'orienter' by default, otherwise use 'mummer'.
+    """
+    
+    def __init__(self, inFileName="", minMatchLength=10, prgToOrient = "orienter", outFileName="", clean=False, verbosity=1):
+        """
+        Constructor.
+        """
+        self._inFileName = inFileName
+        self._minMatchLength = minMatchLength
+        self._prgToOrient = prgToOrient
+        self._outFileName = outFileName
+        self._clean = clean
+        self._verbose = verbosity
+        
+    def help( self ):
+        """
+        Display the help on stdout.
+        """
+        print
+        print "usage:",sys.argv[0].split("/")[-1],"[options]"
+        print "options:"
+        print "     -h: this help"
+        print "     -i: name of the input file (format='fasta')"
+        print "     -m: minimum match length (default=10)"
+        print "     -p: program to use first (default=orienter/mummer)"
+        print "     -o: name of the output file (default=inFileName+'.oriented')"
+        print "     -c: clean"
+        print "     -v: verbosity level (0/default=1/2)"
+        print
+        
+    def setAttributesFromCmdLine( self ):
+        """
+        Set the attributes from the command-line.
+        """
+        try:
+            opts, args = getopt.getopt(sys.argv[1:],"hi:m:p:o:cv:")
+        except getopt.GetoptError, err:
+            print str(err); self.help(); sys.exit(1)
+        for o,a in opts:
+            if o == "-h":
+                self.help(); sys.exit(0)
+            elif o == "-i":
+                self.setInputFileName( a )
+            elif o == "-m":
+                self.setMinMatchLength( a )
+            elif o == "-p":
+                self.setPrgToOrient( a )
+            elif o == "-o":
+                self.setOutputFileName( a )
+            elif o == "-c":
+                self.setClean()
+            elif o == "-v":
+                self.setVerbosityLevel( a )
+                
+    def setInputFileName( self, inFileName ):
+        self._inFileName = inFileName
+        
+    def setMinMatchLength( self, minMatchLength ):
+        self._minMatchLength = int(minMatchLength)
+        
+    def setPrgToOrient( self, prgToOrient ):
+        self._prgToOrient = prgToOrient
+        
+    def setOutputFileName( self, outFileName ):
+        self._outFileName = outFileName
+        
+    def setClean( self ):
+        self._clean = True
+        
+    def setVerbosityLevel( self, verbose ):
+        self._verbose = int(verbose)
+        
+    def checkAttributes( self ):
+        """
+        Check the attributes are valid before running the algorithm.
+        """
+        if self._inFileName == "":
+            print "ERROR: missing input file name"
+            self.help(); sys.exit(1)
+        if not os.path.exists( self._inFileName ):
+            print "ERROR: input file '%s' doesn't exist" % ( self._inFileName )
+            self.help(); sys.exit(1)
+        if self._prgToOrient not in [ "orienter", "mummer" ]:
+            print "ERROR: unknown program '%s'" % ( self._prgToOrient )
+            self.help(); sys.exit(1)
+        if self._outFileName == "":
+            self._outFileName = "%s.oriented" % ( self._inFileName )
+            
+    def useOrienter( self ):
+        """
+        Use 'orienter'.
+        @return: exit value of 'orienter'
+        """
+        prg = "orienter"
+        cmd = prg
+        cmd += " -k"
+#        cmd += " -l %i" % ( self._minMatchLength )
+        cmd += " -v %i" % ( self._verbose )
+        cmd += " %s" % ( self._inFileName )
+        log = os.system( cmd )
+        if log == 0 and self._outFileName.split(".")[-1] != "oriented":
+            os.rename( self._inFileName + ".oriented", self._outFileName )
+        return log
+    
+    def compareInputSequencesWithMummer( self, nbInSeq ):
+        """
+        Launch MUmmer on two single-sequence fasta files to find all maximal matches regardless of their uniqueness and record stdout.
+        Only N(N-1)/2 comparisons are made.
+        @param nbInSeq: number of input sequences
+        @type nbInSeq: integer
+        """
+        if self._verbose > 0:
+            print "aligning input sequences..."
+            sys.stdout.flush()
+        if not CheckerUtils.isExecutableInUserPath( "mummer" ):
+            msg = "ERROR: 'mummer' is not in your PATH"
+            sys.stderr.write( "%s\n" % ( msg ) )
+            sys.exit(1)
+        lInFiles = glob.glob( "batch_*.fa" )
+        for i in range( 1, nbInSeq+1 ):
+            for j in range( i+1, nbInSeq+1 ):
+                if self._verbose > 1:
+                    print "launch MUmmer on %i versus %i" % ( i, j )
+                    sys.stdout.flush()
+                prg = "mummer"
+                cmd = prg
+                cmd += " -maxmatch"
+                cmd += " -l %i" % ( self._minMatchLength )
+                cmd += " -b"
+                cmd += " -F"
+                cmd += " batch_%s.fa" % ( str(j).zfill( len( str( len(lInFiles) ) ) ) )
+                cmd += " batch_%s.fa" % ( str(i).zfill( len( str( len(lInFiles) ) ) ) )
+                cmd += " > mummer_%i_vs_%i.txt" % ( i, j )
+                if self._verbose < 3:
+                    cmd += " 2> /dev/null"
+                returnStatus = os.system( cmd )
+                if returnStatus != 0:
+                    msg = "ERROR: '%s' returned '%i'" % ( prg, returnStatus )
+                    sys.stderr.write( "%s\n" % ( msg ) )
+                    sys.exit(1)
+                    
+    def parseMummerOutput( self, mummerFileName, nameSeq1, nameSeq2 ):
+        """
+        Parse the output from MUmmer.
+        @param mummerFileName: file with the output from MUmmer
+        @type mummerFileName: string
+        @param nameSeq1: name of the first sequence in the pairwise comparison
+        @type nameSeq1: string
+        @param nameSeq2: name of the first sequence in the pairwise comparison
+        @type nameSeq2: string
+        @return: dictionary whose keys are strands and values the number of maximal matches
+        """
+        if self._verbose > 1:
+            print "parse '%s'" % ( mummerFileName )
+            sys.stdout.flush()
+        dStrand2NbMatches = {}
+        mummerF = open( mummerFileName, "r" )
+        strand = "direct"
+        nbMatches = 0
+        line = mummerF.readline()
+        while True:
+            if line == "":
+                break
+            if line[0] == ">":
+                if nameSeq1 not in line:
+                    print "ERROR"
+                    print nameSeq1
+                    print nameSeq2
+                    sys.exit(1)
+                if "Reverse" in line:
+                    dStrand2NbMatches[ strand ] = nbMatches
+                    strand = "reverse"
+                    nbMatches = 0
+            else:
+                nbMatches += 1
+            line = mummerF.readline()
+        dStrand2NbMatches[ strand ] = nbMatches
+        mummerF.close()
+        if self._verbose > 1:
+            print " direct: %i maximal matches" % ( dStrand2NbMatches["direct"] )
+            print " reverse: %i maximal matches" % ( dStrand2NbMatches["reverse"] )
+            sys.stdout.flush()
+        return dStrand2NbMatches
+    
+    def getCumulativeMatchLengthsOnBothStrandForEachPairwiseComparison( self, lInHeaders, nbInSeq ):
+        """
+        For each pairwise comparison, retrieve the number of matches on both strand.
+        @param lInHeaders: list of the sequence headers
+        @type lInHeaders: list of strings
+        @param nbInSeq: number of input sequences
+        @type nbInSeq: integer
+        @return: dictionary whose keys are pairwise comparisons and values are number of matches on both strands
+        """
+        dMatrix = {}
+        for i in range( 1, nbInSeq+1 ):
+            for j in range( i+1, nbInSeq+1 ):
+                pairComp = "%i_vs_%i" % ( i, j )
+                dStrand2NbMatches = self.parseMummerOutput( "mummer_%s.txt" % ( pairComp ), lInHeaders[i-1], lInHeaders[j-1] )
+                dMatrix[ pairComp ] = dStrand2NbMatches
+        return dMatrix
+    
+    def showResultsAsOrienter( self, nbInSeq, dMatrix ):
+        """
+        Not used for the moment but can be useful...
+        """
+        for i in range( 1, nbInSeq+1 ):
+            for j in range( i+1, nbInSeq+1 ):
+                pairComp = "%i_vs_%i" % ( i, j )
+                string = "aligning %i with %i" % ( i, j )
+                string += " %i %i" % ( dMatrix[pairComp]["direct"], dMatrix[pairComp]["reverse"] )
+                string += " max=%i" % ( max( dMatrix[pairComp]["direct"], dMatrix[pairComp]["reverse"] ) )
+                if dMatrix[pairComp]["reverse"] > dMatrix[pairComp]["direct"]:
+                    string += " strand=-"
+                    string += " nb=%i" % ( dMatrix[pairComp]["reverse"] )
+                else:
+                    string += " strand=+"
+                    string += " nb=%i" % ( dMatrix[pairComp]["direct"] )
+                print string; sys.stdout.flush()
+                
+    def getSequencesToReverseFromMatrix( self, dMatrix, lNewHeaders ):
+        """
+        Retrieve the sequences than need to be re-oriented.
+        @param dMatrix: 
+        @type dMatrix: 
+        @param lInHeaders: list of the new sequence headers
+        @type lInHeaders: list of strings
+        @return: list of headers corresponding to sequences than need to be re-oriented
+        """
+        lSeqToOrient = []
+        
+        for i in range( 1, len(lNewHeaders)+1 ):
+            for j in range( i+1, len(lNewHeaders)+1 ):
+                comp = "%i_vs_%i" % ( i, j )
+                nbDirectMatches = dMatrix[ comp ][ "direct" ]
+                nbReverseMatches = dMatrix[ comp ][ "reverse" ]
+                if self._verbose > 1:
+                    print "%s: direct=%i reverse=%i" % ( comp, nbDirectMatches, nbReverseMatches )
+                if nbReverseMatches > nbDirectMatches and lNewHeaders[i-1] not in lSeqToOrient:
+                    if lNewHeaders[ j-1 ] not in lSeqToOrient:
+                        if self._verbose > 2:
+                            "need to reverse '%s'" % ( lNewHeaders[j-1] )
+                        lSeqToOrient.append( lNewHeaders[ j-1 ] )
+        return lSeqToOrient
+    
+    
+    def getSequencesToReverse( self ):
+        """
+        Return a list with the headers of the sequences to reverse. 
+        """
+        lSequenceHeadersToReverse = []
+        
+        if self._prgToOrient == "orienter":
+            exitStatus = self.useOrienter()
+            if exitStatus == 0:
+                self.end()
+                sys.exit(0)
+            if exitStatus != 0:
+                print "\nWARNING: 'orienter' had a problem, switching to 'mummer'"
+                sys.stdout.flush()
+                
+        lInHeaders = pyRepet.seq.fastaDB.dbHeaders( self._inFileName )
+        nbInSeq = len( lInHeaders )
+        if self._verbose > 0:
+            print "nb of input sequences: %i" % ( nbInSeq )
+            sys.stdout.flush()
+            
+        pyRepet.seq.fastaDB.shortenSeqHeaders( self._inFileName, 1 )
+        tmpFileName = "%s.shortH" % ( self._inFileName )
+        lNewHeaders = pyRepet.seq.fastaDB.dbHeaders( tmpFileName )
+        dNew2Init = pyRepet.seq.fastaDB.retrieveLinksNewInitialHeaders( "%slink" % ( tmpFileName ) )
+        
+        pyRepet.seq.fastaDB.dbSplit( tmpFileName, nbSeqPerBatch=1, newDir=True )
+        os.chdir( "batches" )
+        self.compareInputSequencesWithMummer( nbInSeq )
+        dMatrix = self.getCumulativeMatchLengthsOnBothStrandForEachPairwiseComparison( lNewHeaders, nbInSeq )
+        os.chdir( ".." )
+        
+        lNewHeadersToReverse = self.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders )
+        for newH in lNewHeadersToReverse:
+            lSequenceHeadersToReverse.append( dNew2Init[ newH ] )
+        if self._verbose > 0:
+            print "nb of sequences to reverse: %i" % ( len(lNewHeadersToReverse) )
+            for initH in lSequenceHeadersToReverse: print " %s" % ( initH )
+            sys.stdout.flush()
+            
+        if self._clean:
+            os.remove( tmpFileName )
+            os.remove( "%slink" % ( tmpFileName ) )
+            
+        return lSequenceHeadersToReverse
+    
+    def orientInputSequences( self, lSequenceHeadersToReverse, tmpFileName="" ):
+        """
+        Save input sequences while re-orienting those needing it.
+        @param lSequenceHeadersToReverse: list of headers corresponding to sequences than need to be re-oriented
+        @type lSequenceHeadersToReverse: list of strings
+        @param tmpFileName: name of a fasta file (inFileName by default)
+        @type tmpFileName: string
+        """
+        if self._verbose > 0:
+            print "saving oriented sequences..."
+            sys.stdout.flush()
+        if tmpFileName == "":
+            tmpFileName = self._inFileName
+        inDB = BioseqDB( tmpFileName )
+        outDB = BioseqDB()
+        for bs in inDB.db:
+            if bs.header in lSequenceHeadersToReverse:
+                bs.reverseComplement()
+                bs.header += " re-oriented"
+            outDB.add( bs )
+        outDB.save( self._outFileName )
+        
+    def clean( self ):
+        if os.path.exists( "batches" ):
+            os.system( "rm -rf batches" )
+        if os.path.exists( "orienter_error.log" ):
+            os.remove( "orienter_error.log" )
+        for f in glob.glob( "core.*" ):
+            os.remove( f )
+            
+    def start( self ):
+        """
+        Useful commands before running the program.
+        """
+        self.checkAttributes()
+        if self._verbose > 0:
+            print "START %s" % ( type(self).__name__ )
+            print "input file: %s" % ( self._inFileName )
+            sys.stdout.flush()
+            
+    def end( self ):
+        """
+        Useful commands before ending the program.
+        """
+        if self._clean:
+            self.clean()
+        if self._verbose > 0:
+            print "END %s" % ( type(self).__name__ )
+            sys.stdout.flush()
+            
+    def run( self ):
+        """
+        Run the program.
+        """
+        self.start()
+        lSequenceHeadersToReverse = self.getSequencesToReverse()
+        self.orientInputSequences( lSequenceHeadersToReverse )
+        self.end()
+        
+if __name__ == "__main__":
+    i = OrientSequences()
+    i.setAttributesFromCmdLine()
+    i.run()