annotate commons/core/parsing/Multifasta2SNPFile.py @ 6:769e306b7933

Change the repository level.

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)