--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/Multifasta2SNPFile.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,846 @@
+import re
+import os
+import logging
+from commons.core.utils.FileUtils import FileUtils
+from commons.core.seq.BioseqDB import BioseqDB
+from commons.core.seq.Bioseq import Bioseq
+from commons.core.LoggerFactory import LoggerFactory
+
+DNA_ALPHABET_WITH_N_AND_DELS = set (['A','T','G','C','N','-'])
+IUPAC = set(['A','T','G','C','U','R','Y','M','K','W','S','B','D','H','V','N', '-', 'a','t','g','c','u','r','y','m','k','w','s','b','d','h','v','n'])
+
+class Multifasta2SNPFile( object ):
+
+    POLYM_TYPE_4_SNP = "SNP"
+    POLYM_TYPE_4_INSERTION = "INSERTION"
+    POLYM_TYPE_4_DELETION = "DELETION"
+    POLYM_DEFAULT_CONFIDENCE_VALUE = "A"
+    SNP_LENGTH = 1
+    FLANK_LENGTH = 250
+    
+    def __init__(self, taxon, batchName="", geneName=""):
+        
+        if(batchName):
+            self._batchName = batchName
+            
+        if(geneName):
+            self._geneName = geneName
+
+        self._taxon = taxon
+        self._outSubSNPFileName = "SubSNP.csv"
+        self._outAlleleFileName = "Allele.csv"
+        self._outIndividualFileName = "Individual.csv"
+        self._outSequenceFSAFileName = "Sequences.fsa"
+        self._outSequenceCSVFileName = "Sequences.csv"
+        self._outBatchFileName = "Batch.txt"
+        self._outBatchLineFileName = "BatchLine.csv"
+        self._logFileName = "multifasta2SNP.log"
+        
+        self._lBatchFileResults = []
+        self._lSubSNPFileResults = []
+        self._lRefSequences = []
+        self._lIndividualFileResults = []
+        self._lBatchLineFileResults = []
+        self._dIndividualNumbers4SubSNPResults = {}
+        self._dAlleleFileResults = {}
+        
+        
+        self.dcurrentIndel = {}
+        self.lIndelsOfTheCurrentLine = []
+        self.lIndelsOverAllLines = []
+        self.dSNPsPositions = {}
+        
+        self._iCurrentLineNumber = 0
+        self._currentBatchNumber = 1
+        self.currentLineName = ""
+        self.currentNucleotide = ""
+        self.currentPosition = 0
+        self._sPolymConfidenceValue = Multifasta2SNPFile.POLYM_DEFAULT_CONFIDENCE_VALUE        
+        self._sPolymType = Multifasta2SNPFile.POLYM_TYPE_4_SNP
+        self._iPolymLength = Multifasta2SNPFile.SNP_LENGTH
+        self._fileUtils = FileUtils()
+        
+        if self._fileUtils.isRessourceExists(self._logFileName):
+            os.remove(self._logFileName)
+        self._logFile = LoggerFactory.createLogger(self._logFileName, logging.INFO, "%(asctime)s %(levelname)s: %(message)s")
+   
+    def runOneBatch( self, inFileName):
+        self._currentFileName = inFileName
+        #TODO: methode a virer; n'utiliser au final que runOneBatchWithoutWriting
+        self._wrapper = self.createWrapperFromFile(inFileName)
+        self._lBatchFileResults = self.completeBatchList()
+        self.detectSNPsAndIndels(self._wrapper) 
+        self._writeAllOutputFiles()
+        self._currentBatchNumber += 1
+        
+    def runOneBatchWithoutWriting( self, inFileName):
+        self.lIndelsOverAllLines = []
+        self._currentFileName = inFileName
+        self._wrapper = self.createWrapperFromFile(inFileName)
+        self._lBatchFileResults = self.completeBatchList()
+        self.detectSNPsAndIndels(self._wrapper) 
+        self._currentBatchNumber += 1
+    
+
+    def _cleanOutputsInTheCurrentDir(self):
+        #TODO: create a list of files to be deleted
+        FileUtils.removeFilesByPattern("*.csv")
+        if (FileUtils.isRessourceExists(self._outBatchFileName)):
+            os.remove(self._outBatchFileName)
+        if (FileUtils.isRessourceExists(self._outSequenceFSAFileName)):
+            os.remove(self._outSequenceFSAFileName)
+
+
+    def _createOutputObjectsIteratingOnCurrentDir(self):
+        #TODO: gerer les extensions multiples
+        extList = [".fasta", ".fsa"]
+        for dirname, dirnames, filenames in os.walk("."):
+            filenames.sort()
+            for filename in filenames:
+                if os.path.splitext(filename)[1] in extList:
+                    self._geneName = os.path.splitext(filename)[0]
+                    self._batchName = "Batch_" + self._geneName
+                    self.runOneBatchWithoutWriting(filename)
+
+    def runSeveralBatches( self, inputDir):
+        #TODO: enlever les chdirs, appeler les fichiers en absolu et modifier les tests en consequences
+        os.chdir(inputDir)
+        self._cleanOutputsInTheCurrentDir()
+        self._createOutputObjectsIteratingOnCurrentDir()
+        self._writeAllOutputFiles()
+        os.chdir("../")
+
+
+    def _treatADeletionClosingWithAnotherBaseThanRefSeq(self, lineName, nucleotide, position):
+        if (self.isTheIndelOpen4ThisLine):
+            self._closeTheCurrentIndel(lineName, nucleotide, position)
+        self._manageSNPs(lineName, nucleotide, position)
+        self.addOnePolymorphicPosition(position)
+
+    def _treatNucleotideDifferentThanRefSeqCase(self, refSeq, lineName, index, nucleotide, position):
+        if (nucleotide == "-" or refSeq[index] == "-"):
+            if (self.isTheIndelOpen4ThisLine):
+                self._expandTheCurrentIndel(position, nucleotide)
+            else:
+                self._startAnIndel(position, nucleotide)
+        else:
+            self._treatADeletionClosingWithAnotherBaseThanRefSeq(lineName, nucleotide, position)
+
+
+    def _treatSameNucleotideInOneIndel(self, refSeq, lineName, index, nucleotide, position):
+        if (self._sPolymType == Multifasta2SNPFile.POLYM_TYPE_4_DELETION):
+            self._closeTheCurrentIndel(lineName, nucleotide, position)
+        elif (self._sPolymType == Multifasta2SNPFile.POLYM_TYPE_4_INSERTION):
+            if (refSeq[index] == "-"):
+                self._expandTheCurrentIndel(position, nucleotide)
+            else:
+                self._closeTheCurrentIndel(lineName, nucleotide, position)
+
+    def detectSNPsAndIndels(self, iRefAndLines):
+        refSeq = iRefAndLines.getReferenceSequence()
+        refSeqLength = len ( refSeq )
+        self.dSNPsPositions = {}
+        
+        for iLineBioseq in iRefAndLines.getLinesBioseqInstances():
+            lineSequence = iLineBioseq.sequence
+            self.currentLineName = iLineBioseq.header
+            self._manageCurrentIndividual(self.currentLineName)
+            
+            index = 0
+            self.isTheIndelOpen4ThisLine = 0
+            self.lIndelsOfTheCurrentLine = []
+            for nucleotide in lineSequence:
+                position = index + 1
+                if  (index <  refSeqLength) and self._isSNPDetected(refSeq, index, nucleotide):
+                    self._treatNucleotideDifferentThanRefSeqCase(refSeq, self.currentLineName, index, nucleotide, position)
+                elif(index <  refSeqLength and self.isTheIndelOpen4ThisLine) :
+                    self._treatSameNucleotideInOneIndel(refSeq, self.currentLineName, index, nucleotide, position)
+                index = index + 1
+                self.currentNucleotide = nucleotide
+                self.currentPosition = position
+                
+            self.lIndelsOverAllLines = self.lIndelsOverAllLines + self.lIndelsOfTheCurrentLine
+        
+        self._postTraitementDetectSNP(self.currentLineName, self.currentNucleotide, self.currentPosition)
+        
+    def _manageCurrentIndividual(self, lineName):
+        self._lIndividualFileResults = self._completeIndividualListWithCurrentIndividual(self._lIndividualFileResults, lineName)
+        self._lBatchLineFileResults = self._completeBatchLineListWithCurrentIndividual(self._lBatchLineFileResults, self._lIndividualFileResults, lineName)
+        if not self._dIndividualNumbers4SubSNPResults.__contains__(lineName):
+            self._dIndividualNumbers4SubSNPResults[lineName] = len(self._lIndividualFileResults)
+        
+
+    def _manageLastPositionIndels(self, lineName, nucleotide, position):
+        if (self.isTheIndelOpen4ThisLine):
+            self._closeTheCurrentIndel(lineName, nucleotide, position)
+            self.lIndelsOverAllLines.append(self.lIndelsOfTheCurrentLine.pop())
+
+    def _postTraitementDetectSNP(self, lineName, nucleotide, position):
+        self._manageLastPositionIndels(lineName, nucleotide, position)
+            
+        self._mergeAllelesAndSubSNPsFromOverlappingIndels()
+        self._addMissingsAllelesAndSubSNPs()
+        
+        self._lSubSNPFileResults = self._sortSubSNPResultByBatchPositionAndLineName(self._lSubSNPFileResults)
+
+    def _manageSNPs(self, lineName, nucleotide, position):
+        self._dAlleleFileResults = self._completeAlleleSetWithCurrentAllele(self._dAlleleFileResults, nucleotide)
+        truePosition = self.getUngappedPositionInRefSeq(position)
+        subSNPName = self._formatSubSNPName(lineName, truePosition, Multifasta2SNPFile.POLYM_TYPE_4_SNP)
+        iAlleleNumber = self._dAlleleFileResults[nucleotide]
+        self._sPolymType = Multifasta2SNPFile.POLYM_TYPE_4_SNP
+        flank5Prime, flank3Prime = self.getFlanksOfASubSNP(lineName, position, Multifasta2SNPFile.SNP_LENGTH, Multifasta2SNPFile.FLANK_LENGTH)
+        dSubSNPResult = {'subSNPName':subSNPName, 'position':truePosition, 'lineName':self._dIndividualNumbers4SubSNPResults[lineName],
+                         'allele':iAlleleNumber, 'batchNumber': self._currentBatchNumber, 'confidenceValue':self._sPolymConfidenceValue,
+                         'type':self._sPolymType, 'length': Multifasta2SNPFile.SNP_LENGTH, 
+                         '5flank':flank5Prime, '3flank':flank3Prime}
+        if(not self.subSNPExistsInSubSNPList(dSubSNPResult, self._lSubSNPFileResults)):
+            self._lSubSNPFileResults.append(dSubSNPResult)
+        
+    def _startAnIndel(self, position, nucleotide):
+        self.dcurrentIndel['start'] = position
+        self.dcurrentIndel['end'] = position
+        self.sCurrentIndelAllele = nucleotide
+        if(nucleotide == "-"):
+            self._sPolymType = Multifasta2SNPFile.POLYM_TYPE_4_DELETION
+        else:
+            self._sPolymType = Multifasta2SNPFile.POLYM_TYPE_4_INSERTION
+        self.isTheIndelOpen4ThisLine = 1
+            
+    def _expandTheCurrentIndel(self, position, nucleotide):
+        self.sCurrentIndelAllele = self.sCurrentIndelAllele + nucleotide
+        self.dcurrentIndel['end'] = position
+        
+    def _closeTheCurrentIndel(self, lineName, nucleotide, position):
+        subSNPName = self._formatSubSNPName(lineName, self.dcurrentIndel['start'], self._sPolymType)
+        
+        dIndel4TheLine = {'name': subSNPName, 'lineName': lineName, 'start': self.dcurrentIndel['start'],'end' :self.dcurrentIndel['end'],
+                          'allele': self.sCurrentIndelAllele, 'type': self._sPolymType, 'length': self._iPolymLength}
+        
+        dIndel4TheLine['length'] = self.getAnIndelLength(dIndel4TheLine)
+        
+        self.lIndelsOfTheCurrentLine.append(dIndel4TheLine)
+        
+        self.dcurrentIndel.clear()
+        self.isTheIndelOpen4ThisLine = 0
+           
+        
+    def _mergeAllelesAndSubSNPsFromOverlappingIndels(self):
+        lIndelList = []
+        for dIndel in self.lIndelsOverAllLines:
+            lIndelList = self.clusteriseIndels(dIndel, self.lIndelsOverAllLines)
+        
+        for dIndel in lIndelList:
+            oldAllele = dIndel['allele']
+            start = dIndel['start']
+            stop = dIndel['end']
+            lineName = dIndel['lineName']
+            
+            LineBioSeq = self._wrapper._iLinesBioseqDB.fetch(lineName)
+            dIndel = self.updateAllele(oldAllele, start, stop, LineBioSeq, dIndel)
+            dSubSNPResult = self.createSubSNPFromAMissingPolym(dIndel, lineName)
+            if(not self.subSNPExistsInSubSNPList(dSubSNPResult, self._lSubSNPFileResults)):
+                self._lSubSNPFileResults.append(dSubSNPResult)
+
+    def updateAllele(self, oldAllele, start, stop, LineBioSeq, dIndel):
+        #TODO: creer le test        
+        newAllele = LineBioSeq.subseq(start, stop).sequence
+        if newAllele != oldAllele:
+            dIndel['allele'] = newAllele
+        self._dAlleleFileResults = self._completeAlleleSetWithCurrentAllele(self._dAlleleFileResults, newAllele)
+        return dIndel
+    
+
+    def getFlanksOfASubSNP(self, lineName, subsnpPosition, polymLength, flankLength):
+        bioSeqOfTheLine = self._wrapper._iLinesBioseqDB.fetch(lineName)
+        flank5Prime = bioSeqOfTheLine.get5PrimeFlank(subsnpPosition, flankLength)
+        flank3Prime = bioSeqOfTheLine.get3PrimeFlank(subsnpPosition, flankLength, polymLength)
+        
+        return flank5Prime, flank3Prime
+
+    def createSubSNPFromAMissingPolym(self, dIndel, lineName):
+        if(dIndel['type'] == Multifasta2SNPFile.POLYM_TYPE_4_INSERTION):
+            start = self.getUngappedPositionInRefSeq(dIndel['start']-1)
+        else:
+            start = self.getUngappedPositionInRefSeq(dIndel['start'])
+            
+        subSNPName = self._formatSubSNPName(dIndel['lineName'], start, dIndel['type'])
+            
+        iAlleleNumber = self._dAlleleFileResults[dIndel['allele']]
+        
+        iPolymLength = self.getAnIndelLength(dIndel)
+        
+        flank5Prime, flank3Prime = self.getFlanksOfASubSNP(lineName, dIndel['start'], iPolymLength, Multifasta2SNPFile.FLANK_LENGTH)
+
+        dSubSNPResult = {'subSNPName':subSNPName, 'position':start, 'lineName':self._dIndividualNumbers4SubSNPResults[lineName], 'allele':iAlleleNumber,
+                         'batchNumber': self._currentBatchNumber, 'confidenceValue':self._sPolymConfidenceValue, 'type':dIndel['type'], 
+                         'length': iPolymLength, '5flank':flank5Prime, '3flank':flank3Prime}
+        
+        return dSubSNPResult
+            
+    def clusteriseIndels(self, dIndel, lIndelsOverAllLines):
+        iIndice = 0
+        for dIndel in lIndelsOverAllLines:
+            iIndice2Compare = 0            
+            for dIndel2Compare in lIndelsOverAllLines:
+                dIndel, dIndel2Compare = self.mergeBoundsForTwoOverlappingIndels(dIndel, dIndel2Compare)
+                lIndelsOverAllLines = self.updateBoundsForAnIndelInAnIndelList(lIndelsOverAllLines, dIndel)
+                lIndelsOverAllLines = self.updateBoundsForAnIndelInAnIndelList(lIndelsOverAllLines, dIndel2Compare)
+                iIndice2Compare = iIndice2Compare + 1
+            iIndice = iIndice + 1
+        
+        return lIndelsOverAllLines
+    
+    def mergeBoundsForTwoOverlappingIndels(self, dIndel1, dIndel2):
+        if((dIndel2['start'] <= dIndel1['start']) and (dIndel2['end'] >= dIndel1['start']) or
+           (dIndel1['start'] <= dIndel2['start']) and (dIndel1['end'] >= dIndel2['start'])):
+            if(dIndel1['start'] <= dIndel2['start']):
+                iStart = dIndel1['start']
+            else:
+                iStart = dIndel2['start']
+            
+            if(dIndel1['end'] >= dIndel2['end']):
+                iEnd = dIndel1['end']
+            else:
+                iEnd = dIndel2['end']
+            
+            dIndel1['start'] = iStart
+            dIndel1['end'] = iEnd
+            dIndel2['start'] = iStart
+            dIndel2['end'] = iEnd            
+        
+        return dIndel1, dIndel2
+                    
+    def updateBoundsForAnIndelInAnIndelList(self, lIndelsList, dIndelWithNewBounds):
+        name = dIndelWithNewBounds['name']
+        dIndelInTheList, iIndice = self.findAnIndelInAListWithHisName(name, lIndelsList)
+        lIndelsList.remove(dIndelInTheList)
+        lIndelsList.insert(iIndice, dIndelWithNewBounds)
+        return lIndelsList
+        
+        
+    def findASubSNPInAListWithHisName(self, name, lSubSNPList):
+        dSubSNP2Find = {}
+        indice = 0
+        indice2Find = -1
+        for dSubSNP in lSubSNPList:            
+            if(dSubSNP['subSNPName'] == name):
+                dSubSNP2Find =  dSubSNP
+                indice2Find = indice
+            indice = indice + 1
+        
+        if dSubSNP2Find == {} or indice2Find == -1:
+            msg = "trying to find a SubSNP not existing: " + name
+            self._logFile.error(msg)
+            raise Exception ("trying to find a SubSNP not existing: " + name)
+        else:
+            return dSubSNP2Find, indice2Find
+        
+    def subSNPExistsInSubSNPList(self, dSubSNP2Find, lSubSNPList):
+        flag = 0
+        for dSubSNP in lSubSNPList:
+            if(dSubSNP2Find['subSNPName'] == dSubSNP['subSNPName']):
+                flag = 1
+        
+        if flag == 1:
+            return True
+        else:
+            return False
+        
+        
+    def findAnIndelInAListWithHisName(self, name, lIndelList):
+        dIndel2Find = {}
+        indice = 0
+        indice2Find = -1
+        for dIndel in lIndelList:            
+            if(dIndel['name'] == name):
+                dIndel2Find =  dIndel
+                indice2Find = indice
+            indice = indice + 1
+        
+        if dIndel2Find == {} or indice2Find == -1:
+            msg = "trying to find an indel not existing: " + name
+            self._logFile.error(msg)
+            raise Exception (msg)
+        else:
+            return dIndel2Find, indice2Find
+        
+    def _addMissingsAllelesAndSubSNPs(self):
+        for dIndel in self.lIndelsOverAllLines:
+                start = dIndel['start']
+                end = dIndel['end']
+                type = dIndel['type']
+                self.addMissingAllelesAndSubSNPsForOnePolym(start, end, type)
+        
+        for position in self.dSNPsPositions:
+            self.addMissingAllelesAndSubSNPsForOnePolym(position, position, "SNP")
+                 
+    def addMissingAllelesAndSubSNPsForOnePolym(self, start, end, polymType):
+        refSeqAllele = self._wrapper._iReferenceBioseq.subseq(start, end).sequence
+        BioSeqDb = self._wrapper.getLinesBioseqInstances()
+        lBioSeqDbAlleles = self.getAllelesOfASubSeq(BioSeqDb, start, end)
+        for subSequence in lBioSeqDbAlleles:
+            if(subSequence['allele'] == refSeqAllele):
+                lineName = subSequence['header']
+                dMissingPolym = {'lineName': lineName, 'start': start,'end' :end,
+                          'allele': subSequence['allele'], 'type':polymType}
+                self._dAlleleFileResults = self._completeAlleleSetWithCurrentAllele(self._dAlleleFileResults, subSequence['allele'])
+                dSubSNPResult = self.createSubSNPFromAMissingPolym(dMissingPolym, lineName)
+                if(not self.subSNPExistsInSubSNPList(dSubSNPResult, self._lSubSNPFileResults)):
+                    self._lSubSNPFileResults.append(dSubSNPResult) 
+                    
+    def addOnePolymorphicPosition(self, position):
+        if(not self.dSNPsPositions.has_key(position)):
+            self.dSNPsPositions[position] = 1
+            
+    def getUngappedPositionInRefSeq(self, position):
+        if(position ==1):
+            nbOfGaps = 0
+        else:
+            seqIn5Prime = self._wrapper._iReferenceBioseq.subseq(1, position-1).sequence
+            nbOfGaps = seqIn5Prime.count("-")  
+        
+        return position - nbOfGaps
+        
+    def getAllelesOfASubSeq(self, BioSeqDb, start, end):
+        lAlleles = []
+        for iBioSeq in BioSeqDb:
+            dAlleles = {}
+            dAlleles['header'] = iBioSeq.header
+            dAlleles['allele'] = iBioSeq.subseq(start, end).sequence
+            lAlleles.append(dAlleles)
+        
+        return lAlleles
+    
+    def getAnIndelLength(self, dIndel):
+        length = 0        
+        if(dIndel['type'] == Multifasta2SNPFile.POLYM_TYPE_4_DELETION):
+            length = dIndel['end'] - dIndel['start'] + 1
+        else:
+            length = len(dIndel['allele'])
+        
+        return length
+            
+    def createWrapperFromFile(self, inFileName):        
+        faF = open(inFileName, "r")
+        iBioSeqDB = self._extractSequencesFromInputFile(faF)
+        faF.close()
+
+        iBioSeqDB.upCase()
+        referenceBioseq = iBioSeqDB[0]
+        linesBioSeqDB = iBioSeqDB.extractPart(1, iBioSeqDB.getSize() - 1)
+        
+        try:
+            if(FileUtils.isEmpty(inFileName)):
+                msg = "The input file is empty!"
+                self._logFile.error(self._prefixeWithLineNumber (msg))
+                raise Exception (self._prefixeWithFileName (msg))
+            if(self.isHeaderInRefSeqList(referenceBioseq.header)):
+                msg = "This reference sequence already exists in one previous file!"
+                self._logFile.error(self._prefixeWithLineNumber (msg))
+                raise Exception (self._prefixeWithLineNumber (msg))
+        except Exception, e :
+            raise Exception ("Problem with one input file: \n" + str(e))
+        
+        self._lRefSequences.append(referenceBioseq)
+        
+        return  ReferenceBioseqAndLinesBioseqDBWrapper(referenceBioseq, linesBioSeqDB, self._logFile, inFileName)
+    
+    def isHeaderInRefSeqList(self, header):
+        isHeader = False
+        for item in self._lRefSequences:
+            if item.header == header:
+                isHeader = True  
+        return isHeader
+                
+    def completeBatchList(self):
+        dBatchResults = {'BatchNumber' : self._currentBatchNumber, 'BatchName' : self._batchName, 'GeneName' : self._geneName,'ContactNumber' : "1", 
+                         'ProtocolNumber' : "1", 'ThematicNumber' : "1", 'RefSeqName': self._wrapper._iReferenceBioseq.header}
+        
+        self._lBatchFileResults.append(dBatchResults)
+        
+        return self._lBatchFileResults
+       
+    def getLineAsAHeader(self, lineToBeCheck, lineNumber = 0):
+        """
+        header line begin with the tag(or token) '>' tag 
+                    ended with an carriage return
+                    contain The name of sequence must respect this alphabet [a-zA-Z0-9_-:]
+        """
+        obsHeader = lineToBeCheck
+        if obsHeader[0]!=">" :
+            msg = "tag '>' omitted before header"
+            self._logFile.error(self._prefixeWithLineNumber (msg))
+            raise Exception (self._prefixeWithLineNumber (msg))
+        else :
+            obsHeader = obsHeader[1:]
+        obsHeader = obsHeader.replace ("\n","")  
+        obsHeader = self._removeRepeatedBlanksInAStr(obsHeader)
+        obsHeader = self._replaceBlankByUnderScoreInAStr(obsHeader) 
+        if self.checkHeaderAlphabet(obsHeader) :
+            return obsHeader
+        self._logFile.error(self._prefixeWithLineNumber ("fatal error on header"))
+        raise Exception (self._prefixeWithLineNumber ("fatal error on header"))
+    
+    def getLineAsASeq(self, lineToBeCheck):
+        """
+        Sequence line 
+                    ended with an carriage return
+                    contain only character of the IUPAC alphabet
+        """
+        obsSeq = str.upper(lineToBeCheck)
+        obsSeq = obsSeq.replace ("\n","")
+        obsSeq = obsSeq.replace ("\r","")      
+        obsLine = obsSeq.replace("-","")
+        if not self.isIUPAC_bases(obsLine) :
+            msg = "the sequence contain a non nucleic character "
+            self._logFile.error(self._prefixeWithLineNumber (msg))
+            raise Exception (self._prefixeWithLineNumber (msg))
+        return obsSeq
+    
+    def checkHeaderAlphabet( self, strToCheck):
+        """
+        Check the string 
+        the string is not a header when founding a pattern not corresponding to the regexp
+        \W Matches any non-alphanumeric character; this is equivalent to the class [^a-zA-Z0-9_-:]. 
+        """
+        if strToCheck=="":
+            return False      
+        p = re.compile('[^a-zA-Z0-9_:\-]', re.IGNORECASE)  #p = re.compile('(\W|-|:)+', re.IGNORECASE)
+        errList=p.findall(strToCheck)
+        if len( errList ) > 0 :
+            return False
+        else:
+            return True
+        
+    ## Check the string is nucleotides sequence from the DNA_ALPHABET_WITH_N = ["A","T","G","C","N"] of IUPAC nomenclature.
+    #  @return True if sequence contain A, T, G, C or N False otherwise  
+    #  
+    def isDNA_bases( self, sequence):
+        if sequence == "" :
+            return False
+        
+        setFromString = set()
+        
+        for nt in sequence :
+            setFromString.add(nt)
+            
+        return  setFromString.issubset(DNA_ALPHABET_WITH_N_AND_DELS)
+    
+    ## Check if the string is nucleotides sequence from the IUPAC ALPHABET .
+    #  @return True if sequence contain IUPAC letters False otherwise  
+    #  
+    def isIUPAC_bases( self, sequence):
+        if sequence == "" :
+            return False
+        
+        setFromString = set()
+        
+        for nt in sequence :
+            setFromString.add(nt)
+            
+        return  setFromString.issubset(IUPAC)
+    
+    def _writeAllOutputFiles(self):
+        writer = Multifasta2SNPFileWriter()
+        writer.write(self)
+        
+    def _sortSubSNPResultByBatchPositionAndLineName(self, lSubSNPResults):
+        return sorted(lSubSNPResults, key=lambda SNPresults: (SNPresults['batchNumber'], SNPresults['position'], SNPresults['lineName']))    
+    
+    def _formatSubSNPName(self, currentLineHeader, position, polymType):
+        shortPolymType = polymType[:3]
+        return  self._batchName + "_" + shortPolymType + "_" + str(position) + "_" + currentLineHeader
+
+    def _isSNPDetected(self, referenceSequence, index, nt):
+        if((nt != referenceSequence[index]) and (nt.upper() != "N") and (referenceSequence[index].upper() != "N")):
+            return True
+        else:
+            return False
+    
+    def _extractSequencesFromInputFile(self, inFile):
+        # attention :  DNA_ALPHABET_WITH_N_AND_DELS = Set (['A','T','G','C','N']) no including "gap"
+        lInFileLines = inFile.readlines()
+        nbOfLines = len(lInFileLines) - 1
+        #premiere lecture 
+        self._iCurrentLineNumber = 0
+        isSameSeq = False
+        newSeq = ""
+        bioseqDB = BioseqDB ()
+        while self._iCurrentLineNumber < nbOfLines :
+            bioseq = Bioseq()
+            bioseq.header = self.getLineAsAHeader( lInFileLines[self._iCurrentLineNumber] )
+            isSameSeq = True
+            while isSameSeq and (self._iCurrentLineNumber < nbOfLines) :
+                self._iCurrentLineNumber +=1
+                if lInFileLines[self._iCurrentLineNumber][0] == ">" :
+                    isSameSeq = False
+                else :
+                    newSeq = newSeq + self.getLineAsASeq( lInFileLines[self._iCurrentLineNumber] )
+                    isSameSeq = True
+            bioseq.setSequence(newSeq)
+            newSeq = ""
+            bioseqDB.add(bioseq)
+        return bioseqDB
+    
+    def _removeRepeatedBlanksInAStr (self, StrToClean ):
+        resStr=StrToClean.expandtabs(2)
+        compResStr=resStr.replace ("  "," ")
+        while compResStr != resStr :
+            resStr=compResStr
+            compResStr=resStr.replace ("  "," ")
+        return resStr  
+    
+    def _replaceBlankByUnderScoreInAStr (self, StrToClean ):
+        resStr = StrToClean.replace (" ","_")  
+        return resStr
+          
+    def _prefixeWithLineNumber (self, strMsg):
+        resStr = "File: " + self._currentFileName + "\t"
+        resStr += "Line %i " % (self._iCurrentLineNumber+1 ) + strMsg
+        return resStr
+    
+    def _prefixeWithFileName (self, strMsg):
+        resStr = "File: " + self._currentFileName + "\n" + strMsg
+        return resStr
+
+    
+    def _completeAlleleSetWithCurrentAllele(self, dAlleleFileResults, dnaBase):
+        if dAlleleFileResults.has_key(dnaBase):
+            return dAlleleFileResults
+        else:
+            iAlleleNumber = len(dAlleleFileResults) + 1
+            dAlleleFileResults[dnaBase] = iAlleleNumber
+            return dAlleleFileResults
+        
+    def _completeIndividualListWithCurrentIndividual(self, lIndividualResults, lineName):
+        if lIndividualResults == []:
+            iIndividualNumber = 1
+        else:
+            iIndividualNumber = len(lIndividualResults) + 1 
+        
+        #TODO: transformer la liste de dictionnaire en liste d'objets
+        if not (self._checkIfALineExistInList(lIndividualResults, lineName)):
+            dIndividual2Add = {'individualNumber': iIndividualNumber, 'individualName': lineName, 'scientificName': self._taxon}
+            lIndividualResults.append(dIndividual2Add)
+        
+        return lIndividualResults
+    
+    def _completeBatchLineListWithCurrentIndividual(self, lBatchLineResults, lIndividualResults, lineName):
+        lineDict = self._getALineDictFromADictListWithALineName(lIndividualResults, lineName)
+
+        if len(lineDict) != 0:
+            if(lineDict.has_key('individualNumber')):
+                indivNumberOfTheLineDict = lineDict['individualNumber']
+            else:
+                msg = "Problem with the batchLine results construction: individual named " + lineName + " has no individual number!"
+                self._logFile.error(msg)
+                raise Exception (msg)
+        else:
+            msg = "Problem with the batchLine results construction: individual named " + lineName + " not in individual list!"
+            self._logFile.error(msg)
+            raise Exception (msg)
+            
+        dResults2Add = {'IndividualNumber': str(indivNumberOfTheLineDict), 'BatchNumber' : self._currentBatchNumber}
+        lBatchLineResults.append(dResults2Add)
+        return lBatchLineResults
+    
+    def _getALineDictFromADictListWithALineName(self, lDictList, lineName):
+        dictToReturn = {}
+        for myDict in lDictList:
+            if myDict['individualName'] == lineName:
+                dictToReturn = myDict
+        
+        return dictToReturn
+    
+    def _checkIfALineExistInList(self, lDictList, lineName):
+        for myDict in lDictList:
+            if myDict['individualName'] == lineName:
+                return True
+        return False
+    
+    def _getCurrentBatchResult(self):
+        return self._lBatchFileResults[self._currentBatchNumber-1]
+    
+
+        
+    
+class ReferenceBioseqAndLinesBioseqDBWrapper (object):
+         
+    def __init__ (self, iReferenceBioseq, iLinesBioSeqDB, logger, fileName):
+        self._iReferenceBioseq = iReferenceBioseq
+        self._iLinesBioseqDB = iLinesBioSeqDB
+        self._logger = logger
+        self._currentFileName = fileName
+        self._checkAllSeqs()
+
+    
+    def _checkAllSeqs(self):
+        self._iReferenceBioseq.checkEOF()
+        refSeqLen = self._iReferenceBioseq.getLength()
+        
+        for seq in self._iLinesBioseqDB.db:
+            seq.checkEOF()
+            if(not seq.getLength() == refSeqLen):
+                msg = "File: " + self._currentFileName + ", problem with the sequence " + seq.header + ": its length is different from the reference seq! All the sequences must have the same length.\n"
+                msg += "refseq length: " + str(refSeqLen) + "\n"
+                msg += "seq length: " + str(seq.getLength()) + "\n"
+                self._logger.error(msg)
+                raise Exception (msg)
+     
+    def getLinesBioseqInstances(self):
+        return self._iLinesBioseqDB.db
+    
+    def getReferenceSequence(self):
+        return self._iReferenceBioseq.sequence
+    
+class Multifasta2SNPFileWriter(object):
+
+    SUB_SNP_FILE_HEADER = ["SubSNPName","ConfidenceValue","Type","Position","5flank",
+                           "3flank","Length","BatchNumber","IndividualNumber","PrimerType","PrimerNumber","Forward_or_Reverse","AlleleNumber"]
+
+    ALLELE_FILE_HEADER = ["AlleleNumber","Value","Motif","NbCopy","Comment"]
+    
+    INDIVIDUAL_FILE_HEADER = ["IndividualNumber","IndividualName","Description","AberrAneuploide",
+                              "FractionLength","DeletionLineSynthesis","UrlEarImage","TypeLine","ChromNumber","ArmChrom","DeletionBin","ScientificName",
+                              "local_germplasm_name","submitter_code","local_institute","donor_institute","donor_acc_id"]
+    
+    SEQUENCE_CSV_FILE_HEADER = ["SequenceName","SeqType","BankName","BankVersion","ACNumber","Locus","ScientificName"]
+    
+    BATCH_TXT_FILE_HEADER = ["BatchNumber", "BatchName", "GeneName", "Description", "ContactNumber", "ProtocolNumber", "ThematicNumber", "RefSeqName", "AlignmentFileName", "SeqName"]
+    
+    BATCH_LINE_FILE_HEADER = ["IndividualNumber", "Pos5", "Pos3", "BatchNumber", "Sequence"]
+    
+    def __init__(self):
+        self._csvFieldSeparator = ";"
+        self._txtSubFieldSeparator = ": "
+        self._txtFieldSeparator = "\n"
+        self._primerType = "Sequence"
+        self._csvLineSeparator = "\n"
+        self._txtLineSeparator = "//\n"
+        
+    def write(self, iMultifasta2SNPFile):
+        self._writeSubSNPFile(iMultifasta2SNPFile._outSubSNPFileName, iMultifasta2SNPFile._lSubSNPFileResults)
+        self._writeAlleleFile(iMultifasta2SNPFile._outAlleleFileName, iMultifasta2SNPFile._dAlleleFileResults)
+        self._writeIndividualFile(iMultifasta2SNPFile._outIndividualFileName, iMultifasta2SNPFile._lIndividualFileResults)
+        self._writeSequenceFiles(iMultifasta2SNPFile._outSequenceFSAFileName, iMultifasta2SNPFile._outSequenceCSVFileName, iMultifasta2SNPFile._lRefSequences, iMultifasta2SNPFile._taxon)
+        self._writeBatchFile(iMultifasta2SNPFile._outBatchFileName, iMultifasta2SNPFile._lBatchFileResults)
+        self._writeBatchLineFile(iMultifasta2SNPFile._outBatchLineFileName, iMultifasta2SNPFile._lBatchLineFileResults)
+        
+    def sortAlleleResultByAlleleNumber(self, dAlleleFileResults):
+        return sorted(dAlleleFileResults.items(), key=lambda(k,v):(v,k))
+    
+    def _writeSubSNPFile(self, subSNPFileName, lSNP2Write):
+        outF = open(subSNPFileName, "w")
+        self._writeSNPFileHeader(outF)
+        for dSNP in lSNP2Write:
+            self._writeSNPFileLine(outF, dSNP)
+        outF.close()
+    
+    def _writeAlleleFile(self, alleleFileName, dAllele2Write):
+        outF = open(alleleFileName, "w")
+        self._writeAlleleFileHeader(outF)
+        lAlleleSortedResults = self.sortAlleleResultByAlleleNumber(dAllele2Write)
+        for tAllele in lAlleleSortedResults:
+            self._writeAlleleFileLine(outF, tAllele[0], tAllele[1])
+                    
+        outF.close()
+        
+    def _writeIndividualFile(self, individualFileName, lIndividual2Write):
+        sorted(lIndividual2Write, key=lambda Individual: (Individual['individualNumber']))
+        outF = open(individualFileName, "w")
+        self._writeIndividualFileHeader(outF)
+        
+        for dIndiv in lIndividual2Write:
+            self._writeIndividualFileLine(outF, dIndiv)
+                    
+        outF.close()
+        
+    def _writeSequenceFiles(self, sequenceFSAFileName, sequenceCSVFileName, lRefSequences, taxon):
+        outFSA = open(sequenceFSAFileName, "w")
+        outCSV = open(sequenceCSVFileName, "w")
+        self._writeSequenceCSVHeader(outCSV)
+       
+        for refSeq in lRefSequences:
+            refSeq.cleanGap()
+            self._writeSequenceFSAFile(outFSA, refSeq)
+            self._writeSequenceCSVLine(outCSV, refSeq, taxon)
+            
+        outFSA.close()
+        outCSV.close()
+    
+    def _writeSequenceFSAFile(self, outF, refSeq):        
+        outF.write( ">%s\n" % ( refSeq.header ) )
+        outF.write( "%s\n" % ( refSeq.sequence[0:refSeq.getLength()] ) )
+        
+        
+    def _writeBatchFile(self, batchFileName, lBatchResults):
+        outF = open(batchFileName, "w")
+        for dBatchResults in lBatchResults:   
+            for head in Multifasta2SNPFileWriter.BATCH_TXT_FILE_HEADER[:]:
+                if dBatchResults.has_key(head):
+                    outF.write(head + self._txtSubFieldSeparator + str(dBatchResults[head]) + self._txtFieldSeparator)
+                else:
+                    outF.write(head + self._txtSubFieldSeparator + self._txtFieldSeparator)
+                    
+            outF.write(self._txtLineSeparator)
+            
+        outF.close()
+        
+    def _writeBatchLineFile(self, batchLineFileName, lBatchLineResults):
+        outF = open(batchLineFileName, "w")
+        self._writeBatchLineFileHeader(outF)
+        for dResult in lBatchLineResults:
+            self._writeBatchLineFileLine(outF, dResult)
+        outF.close()
+        
+    def _writeSNPFileHeader(self, outF):
+        for head in Multifasta2SNPFileWriter.SUB_SNP_FILE_HEADER[:-1]:
+            outF.write(head + self._csvFieldSeparator)
+        outF.write(Multifasta2SNPFileWriter.SUB_SNP_FILE_HEADER[-1] + self._csvLineSeparator)
+ 
+    def _writeAlleleFileHeader(self, outF):
+        for head in Multifasta2SNPFileWriter.ALLELE_FILE_HEADER[:-1]:
+            outF.write(head + self._csvFieldSeparator)
+        outF.write(Multifasta2SNPFileWriter.ALLELE_FILE_HEADER[-1] + self._csvLineSeparator)
+        
+    def _writeIndividualFileHeader(self, outF):
+        for head in Multifasta2SNPFileWriter.INDIVIDUAL_FILE_HEADER[:-1]:
+            outF.write(head + self._csvFieldSeparator)
+        outF.write(Multifasta2SNPFileWriter.INDIVIDUAL_FILE_HEADER[-1] + self._csvLineSeparator)
+        
+    def _writeSequenceCSVHeader(self, outF):
+        for head in Multifasta2SNPFileWriter.SEQUENCE_CSV_FILE_HEADER[:-1]:
+            outF.write(head + self._csvFieldSeparator)
+        outF.write(Multifasta2SNPFileWriter.SEQUENCE_CSV_FILE_HEADER[-1] + self._csvLineSeparator)
+       
+    def _writeBatchLineFileHeader(self, outF):
+        for head in Multifasta2SNPFileWriter.BATCH_LINE_FILE_HEADER[:-1]:
+            outF.write(head + self._csvFieldSeparator)
+        outF.write(Multifasta2SNPFileWriter.BATCH_LINE_FILE_HEADER[-1] + self._csvLineSeparator)        
+               
+    def _writeSNPFileLine(self, outF, dSNP):
+        outF.write(dSNP['subSNPName'] + self._csvFieldSeparator)
+        outF.write(dSNP['confidenceValue'] + self._csvFieldSeparator + dSNP['type'] + self._csvFieldSeparator)
+        outF.write(str(dSNP['position']) + self._csvFieldSeparator + dSNP['5flank'] + self._csvFieldSeparator + dSNP['3flank'] + self._csvFieldSeparator)
+        outF.write(str(dSNP['length']) + self._csvFieldSeparator + str(dSNP['batchNumber']) + self._csvFieldSeparator)
+        outF.write(str(dSNP['lineName']) + self._csvFieldSeparator)
+        outF.write(self._primerType + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator + str(dSNP['allele']) + self._csvLineSeparator)
+
+    def _writeAlleleFileLine(self, outF, sAllele2Write, iAlleleNumber):
+        outF.write(str(iAlleleNumber) + self._csvFieldSeparator)
+        outF.write(sAllele2Write + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator + self._csvLineSeparator)
+    
+    def _writeIndividualFileLine(self, outF, dIndividual):
+        outF.write(str(dIndividual['individualNumber']) + self._csvFieldSeparator)
+        outF.write(dIndividual['individualName'] + self._csvFieldSeparator + self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator+ self._csvFieldSeparator)
+        outF.write(dIndividual['scientificName'] + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator+ self._csvFieldSeparator + self._csvFieldSeparator + self._csvLineSeparator)
+    
+    def _writeSequenceCSVLine(self, outF, refSeq, taxon):
+        outF.write(refSeq.header + self._csvFieldSeparator)
+        outF.write("Reference" + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator)
+        outF.write(taxon + self._csvLineSeparator)        
+    
+    def _writeBatchLineFileLine(self, outF, dResult):
+        outF.write(str(dResult['IndividualNumber']) + self._csvFieldSeparator + self._csvFieldSeparator + self._csvFieldSeparator)
+        outF.write(str(dResult['BatchNumber']) + self._csvFieldSeparator + self._csvLineSeparator)