diff --git a/SPiPv0.2.r b/SPiPv0.2.r
new file mode 100644
index 0000000..d673df0
--- /dev/null
+++ b/SPiPv0.2.r
@@ -0,0 +1,1755 @@
+#import librairy
+tryCatch({
+library(RCurl)
+},
+	error=function(cond) {
+		message("Here's the original error message:")
+		message(cond)
+		message("*****You need to install \'RCurl\' library")
+})
+
+myOpts <- curlOptions(connecttimeout = 10)
+useOption = rep("Yes",5)
+names(useOption) = c("SPiCE","MES","BP","Cryptic","ESR")
+samPath=NULL
+fastaFile=NULL
+genome="hg19"
+#SPiP arguments
+
+helpMessage="Usage: SPiPv0.2.r\n
+    [Mandatory] \n
+        \t[-I|--input /path/to/inputFile] \n
+        \t\tlist of variants file (.txt or .vcf)\n
+        \t[-O|--output /path/to/outputFile] \n
+        \t\tName of ouput file (.txt)\n
+    [Options] \n
+        \t[-g|--GenomeAssenbly hg19] \n
+        \t\tGenome assembly version (hg19 or hg38) [default= hg19]\n
+        \t[-s|--SamPath /path/to/samtools] \n
+        \t\tPath to samtools, if you want to use Ensembl api keep this argument empty\n
+        \t[-f|--fastaGenome /path/to/fastaGenome] \n
+        \t\tfasta file of genome used by samtools\n
+        \t[-c|--SPiCE]\n
+        \t\tUse of consensus prediction (SPiCE) (Yes/No) [default= Yes]\n
+        \t[-m|--MES]\n
+        \t\tUse of MES prediction in {-20; -13} (Yes/No) [default= Yes]\n
+        \t[-b|--BPP]\n
+        \t\tUse of Branch point prediction (Yes/No) [default= Yes]\n
+        \t[-d|--Cryptic]\n
+        \t\tUse of de Novo/cryptic prediction (Yes/No) [default= Yes]\n
+        \t[-e|--ESR]\n
+        \t\tUse of ESR prediction (Yes/No) [default= Yes]\n
+        \t[-h|--help]\n
+        \t\tprint this help message and exit\n
+   You could : Rscript SPiPv0.2.r -I ./testCrypt.txt -O ./outTestCrypt.txt"
+
+#get script argument
+args <- commandArgs(trailingOnly = TRUE)
+
+if (length(args)<2){message(helpMessage);stop()}
+
+i=1
+while (i < length(args)){
+    if(args[i]=="-I"|args[i]=="--input"){
+        inputFile=args[i+1];i = i+2
+    }else if(args[i]=="-O"|args[i]=="--output"){
+        outputFile=args[i+1];i = i+2
+    }else if(args[i]=="-g"|args[i]=="--GenomeAssenbly"){
+        genome=args[i+1];i = i+2
+    }else if(args[i]=="-s"|args[i]=="--SamPath"){
+        samPath=args[i+1];i = i+2
+    }else if(args[i]=="-f"|args[i]=="--fastaGenome"){
+        fastaFile=args[i+1];i = i+2
+    }else if(args[i]=="-c"|args[i]=="--SPiCE"){
+        useOption["SPiCE"]=args[i+1];i = i+2
+    }else if(args[i]=="-m"|args[i]=="--MES"){
+        useOption["MES"]=args[i+1];i = i+2
+    }else if(args[i]=="-b"|args[i]=="--BPP"){
+        useOption["BP"]=args[i+1];i = i+2
+    }else if(args[i]=="-d"|args[i]=="--Cryptic"){
+        useOption["Cryptic"]=args[i+1];i = i+2
+    }else if(args[i]=="-e"|args[i]=="--ESR"){
+        useOption["ESR"]=args[i+1];i = i+2
+    }else if(args[i]=="-h"|args[i]=="--help"){
+        message(helpMessage);stop()
+    }else{
+        message(paste("********Unknown option:",args[i],"\n"));message(helpMessage);stop()
+    }
+}
+
+#Other argument
+if(genome!="hg19" & genome!="hg38"){
+	message("###########################")
+	message("#Define the assembly genome version (hg19 or hg38)")
+	message("###########################")
+	message(helpMessage)
+	stop()
+}
+
+if(is.null(samPath)){
+	useEnsemblAPI="YES"
+}else{
+	useEnsemblAPI="NO"
+	if(is.null(fastaFile)){
+		message("###########################")
+		message("#No fasta file for samtools")
+		message("###########################")
+        message(helpMessage)
+		stop()
+	}
+}
+
+message('Your options are:')
+message(paste(names(useOption),collapse="\t"))
+message(paste(useOption,collapse="\t"))
+
+#Get Ref files
+wd_R=getwd()
+inputref = paste(wd_R, "/RefFiles",sep="")
+
+load(paste(wd_R, "/RefFiles/RefFiles.RData",sep=""))
+load(paste(wd_R, "/RefFiles/dataRefSeq",genome,".RData",sep=""))
+
+dataRefSeq = dataRefSeq[-grep("_",dataRefSeq$V1),]
+
+mint_GT=sum(as.numeric(as.vector(sub("Min.   :","",summary(ref_score_GT)[1,]))))
+maxt_GT=sum(as.numeric(as.vector(sub("Max.   :","",summary(ref_score_GT)[6,]))))
+mint_GC=sum(as.numeric(as.vector(sub("Min.   :","",summary(ref_score_GC)[1,]))))
+maxt_GC=sum(as.numeric(as.vector(sub("Max.   :","",summary(ref_score_GC)[6,]))))
+mint1=as.numeric(as.vector(sub("Min.   :","",summary(ref_score_AG)[1,1:10])))
+maxt1=as.numeric(as.vector(sub("Max.   :","",summary(ref_score_AG)[6,1:10])))
+
+maxt1=maxt1[order(maxt1,decreasing=T)]
+maxt1=maxt1[1:8]
+maxt1=sum(maxt1)
+
+mint1=mint1[order(mint1,decreasing=F)]
+mint1=mint1[1:8]
+mint1=sum(mint1)
+
+mint2=sum(as.numeric(as.vector(sub("Min.   :","",summary(ref_score_AG)[1,12:15]))))
+maxt2=sum(as.numeric(as.vector(sub("Max.   :","",summary(ref_score_AG)[6,12:15]))))
+
+i_score=NULL
+i_score1=NULL
+i_score2=NULL
+
+dataESR$hexamer = as.character(dataESR$hexamer)
+ESRmotif = dataESR$hexamer[dataESR$Assignment!="N"]
+LEIsc_valuesWA = dataESR$LEIsc_valuesWA
+LEIsc_valuesHA = dataESR$LEIsc_valuesHA
+LEIsc_valuesHM = dataESR$LEIsc_valuesHM
+LEIsc_valuesWD = dataESR$LEIsc_valuesWD
+LEIsc_valuesHD = dataESR$LEIsc_valuesHD
+ESRlistScore = dataESR$ESEseq_or_ESSseqscore
+
+names(LEIsc_valuesWA) <- dataESR$hexamer
+names(LEIsc_valuesHA) <- dataESR$hexamer
+names(LEIsc_valuesHM) <- dataESR$hexamer
+names(LEIsc_valuesWD) <- dataESR$hexamer
+names(LEIsc_valuesHD) <- dataESR$hexamer
+names(ESRlistScore) <- dataESR$hexamer
+indAcc = c(1:11,17:62,68:95)
+indDon = c(1:28,34:74,80:95)
+
+me2x5 = ME2x5$V1
+names(me2x5) <- as.character(ME2x5$V1.1)
+
+inverseDic <- data.frame(V1 = c('T','G','C','A','N'),row.names = c('A','C','G','T','N'))
+inverseDic$V1 <- as.character(inverseDic$V1)
+
+#import data
+
+getTranscriptFromVCF <- function(chrom, pos){
+	if(substr(as.character(chrom),1,3)!="chr"){
+		chrom = paste("chr",chrom,sep="")
+	}
+	transcript = as.character(dataRefSeq[dataRefSeq$V1==chrom & dataRefSeq$V2<=pos & dataRefSeq$V3>=pos,'V4'])
+	if(length(transcript)==0){
+		transcript = "no transcript"
+		return(transcript)
+	}else{
+		return(transcript)
+	}
+}
+
+getMutationFromVCF <- function (REF, ALT){
+	if(as.numeric(regexpr(',',ALT,fixed =TRUE))<0){
+		if(REF=='.'){
+			mut = paste('ins',ALT,sep="")
+		}else if(ALT=='.'){
+			mut = 'del'
+		}else{
+			if(nchar(REF)>1 | nchar(ALT)>1){
+				mut = paste('delins',ALT,sep="")
+			}else{
+				mut = paste(REF,ALT,sep=">")
+			}
+		}
+	}else{
+		ALT = unlist(strsplit(ALT,',',fixed = TRUE))
+		mut=NULL
+		for (i in 1:length(ALT)){
+			if(REF=='.'){
+				mut[i] = paste('ins',ALT[i],sep="")
+			}else if(ALT[i]=='.'){
+				mut[i] = 'del'
+			}else{
+				if(nchar(REF)>1 | nchar(ALT[i])>1){
+					mut[i] = paste('delins',ALT[i],sep="")
+				}else{
+					mut[i] = paste(REF,ALT[i],sep=">")
+				}
+			}
+		}
+	}
+	return(mut)
+}
+
+getPositionFromVCF <- function(POS, REF){
+	if(nchar(REF)>1){
+		start= POS
+		end = POS+(nchar(REF)-1)
+		pos = paste('g.',paste(start,end,sep='_'),sep="")
+	}else{
+		pos = paste('g.',POS,sep="")
+	}
+	return(pos)
+}
+
+getVariantFromVCF <- function(transcript,position,mutation){
+	transPos = paste(unlist(transcript),unlist(position),sep=":")
+	mutation = unlist(mutation)
+	transPosAdj = rep(transPos,length(mutation))
+	variant = paste(transPosAdj,rep(mutation,each = length(transPos)),sep=":")
+	return(variant)
+}
+
+readVCF <- function(dataLine){
+	dataLine = unlist(strsplit(dataLine,split='\t')) #c("CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO")
+	transcript = getTranscriptFromVCF(dataLine[1],as.numeric(dataLine[2]))
+	position = getPositionFromVCF(as.numeric(dataLine[2]),dataLine[4])
+	mutation =getMutationFromVCF(dataLine[4],dataLine[5])
+	variant = getVariantFromVCF(transcript,position,mutation)
+	result <<- list(variant)
+}
+
+fileFormat = tolower(substr(basename(inputFile),nchar(basename(inputFile))-2,nchar(basename(inputFile))))
+
+if(fileFormat=="txt"){
+	data = read.table(inputFile,sep="\t",header=T)
+	if(is.null(data$varID)){
+		message("###########################")
+		message("#Your data doesn't have the varID column")
+		message("###########################")
+		print_help(opt_parser)
+		stop()
+	}
+}else if(fileFormat=="vcf"){
+	data=NULL
+	VCF =readLines(inputFile)
+	VCF = VCF[-grep("#",VCF,fixed=TRUE)]
+	tmp = mapply(readVCF,VCF)
+	data$varID = as.character(unlist(tmp))
+	data$annot = gsub('\t',' ',names(unlist(tmp)),fixed=TRUE)
+	data= as.data.frame(data)
+	if (length(data[grep('no transcript',data[,'varID']),'varID'])>0){
+		message(paste( "I find no transcrit for the mutation:",paste(data[grep('no transcript',data[,'varID']),'varID'],collapse=", ")))
+		data = data[-grep('no transcript',data[,'varID']),]
+	}
+}else{
+	message("###########################")
+	message("#Incorrect format of input, please try again with a txt or vcf file")
+	message("###########################")
+	print_help(opt_parser)
+	stop()
+}
+
+data$Interpretation <- NA
+data$InterConfident <- NA
+data$chr <- NA
+data$strand <- NA
+data$gNomen <- NA
+data$seqPhysio <- NA
+data$seqMutated <- NA
+data$NearestSS <- NA
+data$distSS <- NA
+data$RegType <- NA
+data$SPiCEproba <- NA
+data$SPiCEinter_2thr <- NA
+data$deltaMES <- NA
+data$mutInPBarea <- NA
+data$deltaESRscore <- NA
+data$posCryptMut <- NA
+data$sstypeCryptMut <- NA
+data$nearestSStoCrypt <- NA
+data$nearestPosSStoCrypt <- NA
+data$nearestDistSStoCrypt <- NA
+data$probaCryptMut <- NA
+data$classProbaCryptMut <- NA
+data$posCryptWT <- NA
+data$probaCryptWT <- NA
+data$classProbaCryptWT <- NA
+data$posSSPhysio <- NA
+data$probaSSPhysio <- NA
+data$classProbaSSPhysio <- NA
+data$probaSSPhysioMut <- NA
+data$classProbaSSPhysioMut <- NA
+
+#functions used in this pipeline
+
+getPosSSphysio <- function(transcrit){
+
+	if(dim(dataRefSeq[dataRefSeq$V4==transcrit,])[1]==0){
+		tkmessageBox(message = paste("I don't find the transcript:",transcrit,"in the Refseq database"),
+		icon = "error",type="ok", title="SPiCE alert")
+	}else{
+
+		chr <<- as.character(dataRefSeq[dataRefSeq$V4==transcrit,1])
+		sens <<- as.character(dataRefSeq[dataRefSeq$V4==transcrit,6])
+
+	if(sens=="+"){
+		posStart=dataRefSeq[dataRefSeq$V4==transcrit,2]
+		tailleCum=dataRefSeq[dataRefSeq$V4==transcrit,12]
+		tailleCum=strsplit(as.character(tailleCum),split=",")
+		tailleCum=as.numeric(unlist(tailleCum))
+		posAcc <<- posStart+tailleCum
+		taille=dataRefSeq[dataRefSeq$V4==transcrit,11]
+		taille=strsplit(as.character(taille),split=",")
+		taille=as.numeric(unlist(taille))
+		posDon <<- posAcc+taille
+		if(length(posDon)>1 & length(posAcc)>1){
+			posDon <<- posDon[-length(posDon)]
+			posAcc <<- posAcc[-1]
+		}
+	}else if(sens=="-"){
+		posEnd=dataRefSeq[dataRefSeq$V4==transcrit,2]
+		tailleCum=dataRefSeq[dataRefSeq$V4==transcrit,12]
+		tailleCum=strsplit(as.character(tailleCum),split=",")
+		tailleCum=as.numeric(unlist(tailleCum))
+		posDon <<- posEnd+tailleCum
+		taille=dataRefSeq[dataRefSeq$V4==transcrit,11]
+		taille=strsplit(as.character(taille),split=",")
+		taille=as.numeric(unlist(taille))
+		posAcc <<- posDon+taille
+		if(length(posDon)>1 & length(posAcc)>1){
+			posDon <<- posDon[-1]
+			posAcc <<- posAcc[-length(posAcc)]
+		}
+	}
+	}
+}
+
+getNearestPos <- function(sens, varPos ,posDon, posAcc){
+	varPos1 = varPos[1]
+	distSS2 = NULL
+	varPos2 = NULL
+	if(length(varPos)==2){
+		varPos2 = varPos[2]
+	}
+	posDon = posDon[order(posDon)]
+	posAcc = posAcc[order(posAcc)]
+
+	minPosDon = min(abs(posDon-varPos1 ))
+	minPosAcc = min(abs(posAcc-varPos1 ))
+
+	if(minPosDon<minPosAcc){
+		SstypePhy <<- "donor"
+		if(length( posDon[posDon==(varPos1 + min(abs(posDon-varPos1 )))])==0){
+			nearestPosDon <-posDon[posDon==(varPos1 - min(abs(posDon-varPos1 )))]
+		}else{
+			nearestPosDon <-posDon[posDon==(varPos1 + min(abs(posDon-varPos1 )))]
+		}
+
+		if(sens=="+"){
+			distSS1 <<- varPos1 - nearestPosDon
+			if(length(varPos)==2){
+				distSS2 = varPos2 - nearestPosDon
+			}
+
+			if(varPos1 <= nearestPosDon){
+				nearestPosAcc = posAcc[which(posDon==nearestPosDon)-1]
+				RegType <<- "Exon"
+				distSS1 <<- distSS1 -1
+				if(length(varPos)==2){
+					distSS2 = distSS2 -1
+				}
+			}else{
+				nearestPosAcc = posAcc[which(posDon==nearestPosDon)]
+				RegType <<- "Intron"
+			}
+		}else{
+			distSS1 <<- nearestPosDon - varPos1+1
+			if(length(varPos)==2){
+				distSS2 = nearestPosDon - varPos2+1
+			}
+			if(varPos1 <= nearestPosDon){
+				nearestPosAcc = posAcc[which(posDon==nearestPosDon)]
+				RegType <<- "Intron"
+			}else{
+				nearestPosAcc = posAcc[which(posDon==nearestPosDon)+1]
+				RegType <<- "Exon"
+				distSS1 <<- distSS1 -1
+				if(length(varPos)==2){
+					distSS2 = distSS2 -1
+				}
+			}
+		}
+		if(is.null(distSS2)){
+			if(distSS1>=(-3) & distSS1<=(6)){
+				RegType <<- paste(RegType,"Cons",sep="")
+			}
+		}else{
+			if((distSS1>=(-3) & distSS1<=6) | (distSS2>=(-3) & distSS2<=6) | (distSS1<(-3) & distSS2>6)){
+				RegType <<- paste(RegType,"Cons",sep="")
+			}
+		}
+	}else{
+		SstypePhy <<- "acceptor"
+		if(length( posAcc[posAcc==(varPos1 + min(abs(posAcc-varPos1 )))])==0){
+			nearestPosAcc <-posAcc[posAcc==(varPos1 - min(abs(posAcc-varPos1 )))]
+		}else{
+			nearestPosAcc <-posAcc[posAcc==(varPos1 + min(abs(posAcc-varPos1 )))]
+		}
+		if(sens=="+"){
+			distSS1 <<- varPos1 - nearestPosAcc-1
+			if(length(varPos)==2){
+				distSS2 = varPos2 - nearestPosAcc-1
+			}
+			if(varPos1 <= nearestPosAcc){
+				nearestPosDon = posDon[which(posAcc==nearestPosAcc)]
+				RegType <<- "Intron"
+			}else{
+				nearestPosDon = posDon[which(posAcc==nearestPosAcc)+1]
+				RegType <<- "Exon"
+				distSS1 <<- distSS1 + 1
+				if(length(varPos)==2){
+					distSS2 = distSS2 + 1
+				}
+			}
+		}else{
+			distSS1 <<- nearestPosAcc - varPos1
+			if(length(varPos)==2){
+				distSS2 = nearestPosAcc - varPos2
+			}
+			if(varPos1 <= nearestPosAcc){
+				nearestPosDon = posDon[which(posAcc==nearestPosAcc)-1]
+				RegType <<- "Exon"
+				distSS1 <<- distSS1 + 1
+				if(length(varPos)==2){
+					distSS2 = distSS2 + 1
+				}
+			}else{
+				nearestPosDon = posDon[which(posAcc==nearestPosAcc)]
+				RegType <<- "Intron"
+			}
+		}
+		if(is.null(distSS2)){
+			if(distSS1>=(-12) & distSS1<=2){
+				RegType <<- paste(RegType,"Cons",sep="")
+			}
+			if (distSS1>=(-20) & distSS1<=(-13)){
+				RegType <<- paste(RegType,"PolyTC",sep="")
+			}
+			if (distSS1>=(-44) & distSS1<=(-18)){
+				RegType <<- paste(RegType,"BP",sep="")
+			}
+		}else{
+			if((distSS1>=(-12) & distSS1<=2) | (distSS2>=(-12) & distSS2<=2) | (distSS1<(-12) & distSS2>2)){
+				RegType <<- paste(RegType,"Cons",sep="")
+			}
+			if (distSS1>=(-20) & distSS1<=(-13) | (distSS2>=(-20) & distSS2<=(-13)) | (distSS1<(-20) & distSS2>(-13))){
+				RegType <<- paste(RegType,"PolyTC",sep="")
+			}
+			if (distSS1>=(-44) & distSS1<=(-18) | distSS2>=(-44) & distSS2<=(-18) | (distSS1<(-44) & distSS2>(-18))){
+				RegType <<- paste(RegType,"BP",sep="")
+			}
+		}
+	}
+
+	distSS <<- distSS1
+	distSS2 <<- distSS2
+	nearestPosAll <<- as.numeric(na.omit(c(nearestPosDon,nearestPosAcc)))
+}
+
+getNearestPosCrypt <- function(sens, cryptPos ,posDon, posAcc){
+	nearestPosDon = 0
+	nearestPosAcc = 0
+	posDon = posDon[order(posDon)]
+	posAcc = posAcc[order(posAcc)]
+	minPosDon = min(abs(posDon-cryptPos))
+	minPosAcc = min(abs(posAcc-cryptPos))
+
+	if(minPosDon<minPosAcc){
+		SstypePhyCrypt = "Don"
+		if(length( posDon[posDon==(cryptPos + min(abs(posDon-cryptPos )))])==0){
+			nearestPosDon <-posDon[posDon==(cryptPos - min(abs(posDon-cryptPos )))]
+		}else{
+			nearestPosDon <-posDon[posDon==(cryptPos + min(abs(posDon-cryptPos )))]
+		}
+		if(sens=="+"){
+			distSSc = cryptPos - nearestPosDon
+			if(cryptPos <= nearestPosDon){
+				distSSc = distSSc -1
+			}
+		}else{
+			distSSc = nearestPosDon - cryptPos+1
+			if(cryptPos > nearestPosDon){
+				distSSc = distSSc -1
+			}
+		}
+	}else{
+		SstypePhyCrypt = "Acc"
+		if(length( posAcc[posAcc==(cryptPos + min(abs(posAcc-cryptPos )))])==0){
+			nearestPosAcc <-posAcc[posAcc==(cryptPos - min(abs(posAcc-cryptPos )))]
+		}else{
+			nearestPosAcc <-posAcc[posAcc==(cryptPos + min(abs(posAcc-cryptPos )))]
+		}
+		if(sens=="+"){
+			distSSc = cryptPos - nearestPosAcc-1
+			if(cryptPos > nearestPosAcc){
+				nearestPosDon = posDon[which(posAcc==nearestPosAcc)+1]
+				distSSc = distSSc + 1
+			}
+		}else{
+			distSSc = nearestPosAcc - cryptPos
+			if(cryptPos <= nearestPosAcc){
+				distSSc = distSSc + 1
+			}
+		}
+	}
+	distSScrypt <<- distSSc
+	SstypePhyCrypt <<- SstypePhyCrypt
+	if(SstypePhyCrypt=="Acc"){
+		nearestPosPhyCrypt <<- nearestPosAcc
+	}else{
+		nearestPosPhyCrypt <<- nearestPosDon
+	}
+}
+
+convertcNomenIngNomen <- function(transcrit,posVar){
+
+	sens = as.character(dataRefSeq[dataRefSeq$V4==transcrit,6])
+	posStart=dataRefSeq[dataRefSeq$V4==transcrit,2]
+	tailleExon = as.numeric(unlist(strsplit(as.character(dataRefSeq[dataRefSeq$V4==transcrit,11]),",")))
+	tailleCum=dataRefSeq[dataRefSeq$V4==transcrit,12]
+	tailleCum=strsplit(as.character(tailleCum),split=",")
+	tailleCum=as.numeric(unlist(tailleCum))
+
+	if(sens=="+"){
+
+		gCDSstart = dataRefSeq[dataRefSeq$V4==transcrit,7]
+		gCDSend = dataRefSeq[dataRefSeq$V4==transcrit,8]
+
+		posAcc = posStart+tailleCum + 1
+		posDon = posAcc+tailleExon - 1
+
+		dataConvert=data.frame(idEx=c(1:length(tailleExon )),lenEx=tailleExon,gStart=posAcc,gEnd=posDon,cStart=0,cEnd=0 )
+
+		ExCDSstart=dataConvert$idEx[dataConvert$gStart<=gCDSstart & dataConvert$gEnd>=gCDSstart]
+		ExCDSend=dataConvert$idEx[dataConvert$gStart<=gCDSend & dataConvert$gEnd>=gCDSend ]
+
+		dataConvert$cStart[dataConvert$idEx==ExCDSstart]=dataConvert$gStart[dataConvert$idEx==ExCDSstart]-gCDSstart -1
+		dataConvert$cEnd[dataConvert$idEx==ExCDSstart]=dataConvert$gEnd[dataConvert$idEx==ExCDSstart]-gCDSstart
+
+		if(ExCDSstart < max(dataConvert$idEx)){
+			for (i in seq(from=ExCDSstart+1,to=max(dataConvert$idEx),by=1)){
+				dataConvert$cStart[dataConvert$idEx==i]=dataConvert$cEnd[dataConvert$idEx==(i-1)]+1
+				dataConvert$cEnd[dataConvert$idEx==i]=dataConvert$cStart[dataConvert$idEx==i]+(dataConvert$lenEx[dataConvert$idEx==i]-1)
+			}
+		}
+		if(ExCDSstart > 1){
+			for (i in seq(from=ExCDSstart-1,to=1,by=-1)){
+				dataConvert$cEnd[dataConvert$idEx==i]=dataConvert$cStart[dataConvert$idEx==(i+1)]-1
+				dataConvert$cStart[dataConvert$idEx==i]=dataConvert$cEnd[dataConvert$idEx==i]-(dataConvert$lenEx[dataConvert$idEx==i]-1)
+			}
+		}
+		cStop=dataConvert$cStart[dataConvert$idEx==ExCDSend]+(gCDSend -dataConvert$gStart[dataConvert$idEx==ExCDSend]-1)
+
+		if(length(grep("-",substr(posVar,2,nchar(posVar)),fixed = T))>0){
+			if(length(grep("-",substr(posVar,1,1),fixed = T))>0){
+				posVarSplit=unlist(strsplit(posVar,"-",fixed = T))
+				posVarSplit=c(paste("-",posVarSplit[2],sep=""),posVarSplit[3])
+			}else{
+				posVarSplit=unlist(strsplit(posVar,"-",fixed = T))
+			}
+				posVar1=posVarSplit[1]
+				posVar2=as.numeric(posVarSplit[2])
+			if(length(grep("*",posVar1,fixed = T))>0){
+					posVar1=as.numeric(substr(posVar1,2,nchar(posVar1)))+cStop
+			}else{
+				posVar1=as.numeric(posVar1)
+			}
+			gVar <<- dataConvert$gStart[dataConvert$cStart==posVar1]-posVar2
+
+		}else if(length(grep("+",substr(posVar,2,nchar(posVar)),fixed = T))>0){
+			posVarSplit=unlist(strsplit(posVar,"+",fixed = T))
+			posVar1=posVarSplit[1]
+			posVar2=as.numeric(posVarSplit[2])
+			if(length(grep("*",posVar1,fixed = T))>0){
+				posVar1=as.numeric(substr(posVar1,2,nchar(posVar1)))+cStop
+			}else{
+				posVar1=as.numeric(posVar1)
+			}
+			gVar <<- dataConvert$gEnd[dataConvert$cEnd==posVar1]+posVar2
+
+		}else if(length(grep("-",substr(posVar,1,1),fixed = T))>0){
+			posVar = as.numeric(posVar)
+			if(posVar <=min(dataConvert$cStart)){
+				gVar <<- min(dataConvert$gStart)-(abs(posVar)-abs(min(dataConvert$cStart)))
+			}else{
+				if(abs(posVar)==abs(dataConvert$cEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])){
+					gVar <<- dataConvert$gEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]
+				}else{
+					gVar <<- dataConvert$gStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]+
+					abs(abs(posVar)-abs(dataConvert$cStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])-1)
+				}
+			}
+		}else if(length(grep("*",substr(posVar,1,1),fixed = T))>0){
+			posVar = as.numeric(substr(posVar,2,nchar(posVar)))
+			posVar = posVar + cStop
+			if(posVar >=max(dataConvert$cEnd)){
+				gVar <<- max(dataConvert$gEnd) + (posVar - max(dataConvert$cEnd))
+			}else{
+				if(abs(posVar)==abs(dataConvert$cEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])){
+					gVar <<- dataConvert$gEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]
+				}else{
+					gVar <<- dataConvert$gStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]+
+						(posVar-dataConvert$cStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])
+				}
+			}
+		}else{
+			posVar = as.numeric(posVar)
+			if(abs(posVar)==abs(dataConvert$cEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])){
+				gVar <<- dataConvert$gEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]
+			}else{
+				gVar <<- dataConvert$gStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]+
+			(posVar-dataConvert$cStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])
+			}
+		}
+
+	}else if(sens=="-"){
+
+		gCDSstart = dataRefSeq[dataRefSeq$V4==transcrit,8]
+		gCDSend = dataRefSeq[dataRefSeq$V4==transcrit,7]
+		posDon = posStart+tailleCum + 1
+		posAcc = posDon+tailleExon - 1
+
+		dataConvert=data.frame(idEx=c(length(tailleExon):1),lenEx=tailleExon,gStart=posAcc,gEnd=posDon,cStart=0,cEnd=0 )
+
+		ExCDSstart=dataConvert$idEx[dataConvert$gStart>=gCDSstart & dataConvert$gEnd<=gCDSstart]
+		ExCDSend=dataConvert$idEx[dataConvert$gStart>=gCDSend & dataConvert$gEnd<=gCDSend ]
+
+		dataConvert$cStart[dataConvert$idEx==ExCDSstart]=gCDSstart-dataConvert$gStart[dataConvert$idEx==ExCDSstart]
+		dataConvert$cEnd[dataConvert$idEx==ExCDSstart]=gCDSstart-dataConvert$gEnd[dataConvert$idEx==ExCDSstart]+1
+
+		if(ExCDSstart < max(dataConvert$idEx)){
+			for (i in seq(from=ExCDSstart+1,to=max(dataConvert$idEx),by=1)){
+				dataConvert$cStart[dataConvert$idEx==i]=dataConvert$cEnd[dataConvert$idEx==(i-1)]+1
+				dataConvert$cEnd[dataConvert$idEx==i]=dataConvert$cStart[dataConvert$idEx==i]+(dataConvert$lenEx[dataConvert$idEx==i]-1)
+			}
+		}
+		if(ExCDSstart > 1){
+			for (i in seq(from=ExCDSstart-1,to=1,by=-1)){
+				dataConvert$cEnd[dataConvert$idEx==i]=dataConvert$cStart[dataConvert$idEx==(i+1)]-1
+				dataConvert$cStart[dataConvert$idEx==i]=dataConvert$cEnd[dataConvert$idEx==i]-(dataConvert$lenEx[dataConvert$idEx==i]-1)
+			}
+		}
+
+		cStop=dataConvert$cStart[dataConvert$idEx==ExCDSend]+(dataConvert$gStart[dataConvert$idEx==ExCDSend] -gCDSend-1)
+
+		if(length(grep("-",substr(posVar,2,nchar(posVar)),fixed = T))>0){
+			if(length(grep("-",substr(posVar,1,1),fixed = T))>0){
+				posVarSplit=unlist(strsplit(posVar,"-",fixed = T))
+				posVarSplit=c(paste("-",posVarSplit[2],sep=""),posVarSplit[3])
+			}else{
+				posVarSplit=unlist(strsplit(posVar,"-",fixed = T))
+			}
+			posVar1=posVarSplit[1]
+			posVar2=as.numeric(posVarSplit[2])
+			if(length(grep("*",posVar1,fixed = T))>0){
+				posVar1=as.numeric(substr(posVar1,2,nchar(posVar1)))+cStop
+			}else{
+				posVar1=as.numeric(posVar1)
+			}
+			gVar <<- dataConvert$gStart[dataConvert$cStart==posVar1]+(posVar2)
+
+		}else if(length(grep("+",substr(posVar,2,nchar(posVar)),fixed = T))>0){
+			posVarSplit=unlist(strsplit(posVar,"+",fixed = T))
+			posVar1=posVarSplit[1]
+			posVar2=as.numeric(posVarSplit[2])
+			if(length(grep("*",posVar1,fixed = T))>0){
+				posVar1=as.numeric(substr(posVar1,2,nchar(posVar1)))+cStop
+			}else{
+				posVar1=as.numeric(posVar1)
+			}
+				gVar <<- dataConvert$gEnd[dataConvert$cEnd==posVar1]-posVar2
+
+		}else if(length(grep("-",substr(posVar,1,1),fixed = T))>0){
+			posVar = as.numeric(posVar)
+			if(posVar <=min(dataConvert$cStart)){
+				gVar <<- max(dataConvert$gStart)+(abs(posVar)-abs(min(dataConvert$cStart)))
+			}else{
+				if(abs(posVar)==abs(dataConvert$cEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])){
+					gVar <<- dataConvert$gEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]
+				}else{
+					gVar <<- dataConvert$gStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]-
+					abs(abs(posVar)-abs(dataConvert$cStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]))
+				}
+			}
+		}else if(length(grep("*",substr(posVar,1,1),fixed = T))>0){
+			posVar = as.numeric(substr(posVar,2,nchar(posVar)))
+			posVar = posVar + cStop
+			if(posVar >=min(dataConvert$cEnd)){
+				gVar <<- min(dataConvert$gEnd) - (posVar - max(dataConvert$cEnd))
+			}else{
+				if(abs(posVar)==abs(dataConvert$cEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])){
+					gVar <<- dataConvert$gEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]
+				}else{
+					gVar <<- dataConvert$gStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]-
+						(posVar-dataConvert$cStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])
+				}
+			}
+		}else{
+			posVar = as.numeric(posVar)
+			if(abs(posVar)==abs(dataConvert$cEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])){
+				gVar <<- dataConvert$gEnd[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]
+			}else{
+				if(dataConvert$cStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]<0){
+					gVar <<- dataConvert$gStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]-
+						(posVar-dataConvert$cStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]-1)
+				}else{
+					gVar <<- dataConvert$gStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar]-
+						(posVar-dataConvert$cStart[dataConvert$cStart<=posVar & dataConvert$cEnd>=posVar])
+				}
+			}
+		}
+	}
+}
+
+getRevSeq <- function(sequence){
+	lenSeq = nchar(sequence)
+	seqRev = paste(rep("N",lenSeq),collapse="")
+
+	for(i in 1:lenSeq){
+		substr(seqRev,i,i) = inverseDic[substr(sequence,lenSeq-i+1,lenSeq-i+1),1]
+	}
+	return(seqRev)
+}
+
+getSeqFromSamtools <- function(chromosome,start,end,strand,command,fastaRef){
+	posToAsk <- paste(chromosome,':',start,'-',end,sep="")
+	path2script <- paste('faidx',fastaRef,posToAsk)
+	samtoolsSeq = system2(command, args=path2script, stdout = TRUE)
+	samtoolsSeq = samtoolsSeq[-1]
+
+	if(length(samtoolsSeq)>1){
+		seqDNApool=""
+		for(i in 1:length(samtoolsSeq)){
+			seqDNApool=paste(seqDNApool,samtoolsSeq[i],sep="")
+		}
+		seqDNA = seqDNApool
+	}else{
+		seqDNA = samtoolsSeq
+	}
+
+	seqDNA = toupper(seqDNA)
+	if(strand=="-"){
+		seqDNA = getRevSeq(seqDNA)
+	}
+	return(seqDNA)
+}
+
+getSequencePhysio <- function(genome,sens,chr,start,end){
+	if(useEnsemblAPI=="YES"){
+		if(genome=="hg38"){
+			server = "http://rest.ensembl.org/"
+		}else if(genome=="hg19"){
+		server = "http://grch37.rest.ensembl.org/"
+		}
+
+		if(sens=="+"){
+			urls = paste(server ,"sequence/region/human/",chr,":",start,"..",end,":1.fasta",sep="")
+
+		}else if(sens=="-"){
+			urls = paste(server ,"sequence/region/human/",chr,":",start,"..",end,":-1.fasta",sep="")
+		}
+		seqFasta=""
+		i = 0
+		while(seqFasta==""){
+			try(eval(parse(text="seqFasta = getURL(urls, .opts = myOpts)")))
+			i = i+1
+			if(seqFasta==""){
+				Sys.sleep(3)
+				print(i)
+			}else{
+				seqDNA <<- unlist(strsplit(as.character(seqFasta),"\n"))[-1]
+			}
+		}
+		if(length(seqDNA)>1){
+			seqDNApool=""
+			for(i in 1:length(seqDNA)){
+				seqDNApool=paste(seqDNApool,seqDNA[i],sep="")
+			}
+			seqDNA = seqDNApool
+		}else{
+			seqDNA = seqDNA
+		}
+	}else{
+		command = samPath
+		fastaRef = fastaFile
+		gPos=c(start,end)
+		gPos = gPos[order(gPos)]
+		seqDNA = getSeqFromSamtools(chr, gPos[1], gPos[2], sens, command, fastaRef)
+	}
+	return(seqDNA)
+}
+
+getSequenceMutated <- function(varPos, sens, seqPhysio, ntChange, varType, genome, chr){
+
+	if(varType=="substitution"){
+		ntMut <<- as.character(unlist(strsplit(ntChange,">")))[2]
+		seqMutated <<- paste(substr(seqPhysio,1,150),ntMut,substr(seqPhysio,152,301),sep="")
+	}else if (varType=="del"){
+ 		nbDel <<- abs(varPos[1]-varPos[2])+1
+		if(sens=="+"){
+			seqMutated1 = substr(seqPhysio,1,150)
+			start = varPos[2]+1
+			end = varPos[2]+151
+			seqMutated2=getSequencePhysio (genome,sens,chr,start,end)
+			seqMutated <<- paste(seqMutated1 , seqMutated2,sep="")
+		}else if(sens=="-"){
+			seqMutated1 = substr(seqPhysio,1,150)
+			start=varPos[2]-1
+			end=varPos[2]-151
+			seqMutated2=getSequencePhysio (genome,sens,chr,end,start)
+			seqMutated <<- paste(seqMutated1 , seqMutated2,sep="")
+		}
+	}else if (varType=="ins"){
+
+		ntIns <<- gsub("ins", "", ntChange)
+		nbIns <<- nchar(ntIns)
+		seqMutated <<- paste(substr(seqPhysio,1,151),ntIns,substr(seqPhysio,152,301-nchar(ntIns)),sep="")
+
+	}else if (varType=="dup"){
+
+		nbIns <<- abs(varPos[1]-varPos[2])+1
+		ntIns = substr (seqPhysio,151, 150+nbIns)
+		seqMutated1 = substr(seqPhysio,1, 150)
+		seqMutated2 = substr(seqPhysio,151+nbIns, 301)
+		seqMutated <<- paste(seqMutated1, ntIns, ntIns, seqMutated2,sep="")
+
+	}else if (varType=="delins"){
+
+			nbDel <<- abs(varPos[1]-varPos[2])+1
+			ntIns <<- gsub("delins", "", ntChange)
+			nbIns <<- nchar(ntIns)
+
+		if(sens=="+"){
+
+			seqMutated1 = substr(seqPhysio,1,150)
+			start = varPos[2]+1
+			end = varPos[2]+151
+			seqMutated2 = getSequencePhysio (genome,sens,chr,start,end)
+			seqMutated <<- substr(paste(seqMutated1,ntIns ,seqMutated2,sep=""),1,301)
+
+		}else if(sens=="-"){
+
+			seqMutated1 = substr(seqPhysio,1,150)
+			start = varPos[2]-1
+			end = varPos[2]-151
+			seqMutated2 = getSequencePhysio (genome,sens,chr,end,start)
+			seqMutated <<- substr(paste(seqMutated1,ntIns ,seqMutated2,sep=""),1,301)
+
+		}
+	}
+}
+
+hashseq <- function( seq ){
+	seqnum=gsub("A",0,seq)
+	seqnum=gsub("C",1,seqnum)
+	seqnum=gsub("G",2,seqnum)
+	seqnum=gsub("T",3,seqnum)
+	lenseq=length(seqnum)
+	four=c(1,4,16,64,256,1024,4096,16384)
+	i=1
+	sum=1
+	while(i<=lenseq){
+		sum = sum + (as.numeric(seqnum[i])*four[lenseq-i+1])
+		i=i+1
+	}
+		return(sum)
+}
+
+MESdonor <- function(seqDon){
+	spliseq=unlist(strsplit(seqDon,split=""))
+	valueCons1=cons1$score[cons1$N==spliseq[4]]
+	valueCons2=cons2$score[cons2$N==spliseq[5]]
+	valueN1=bgd$score[bgd$N==spliseq[4]]
+	valueN2=bgd$score[bgd$N==spliseq[5]]
+	valueCan=(valueCons1*valueCons2)/(valueN1*valueN2)
+	seqNcan=paste(spliseq[1],spliseq[2],spliseq[3],spliseq[6],spliseq[7],spliseq[8],spliseq[9],sep="")
+	valueNcan=me2x5[seqNcan]
+	MESscore <<- log(valueNcan*valueCan)/log(2)
+}
+
+MESacceptor <- function(seqAcc){
+	spliseqAcc=unlist(strsplit(seqAcc,split=""))
+	valueCons1_acc=cons1_acc$score[cons1_acc$N==spliseqAcc[19]]
+	valueCons2_acc=cons2_acc$score[cons2_acc$N==spliseqAcc[20]]
+	valueN1_acc=bgd$score[bgd$N==spliseqAcc[19]]
+	valueN2_acc=bgd$score[bgd$N==spliseqAcc[20]]
+	valueCanAcc=(valueCons1_acc*valueCons2_acc)/(valueN1_acc*valueN2_acc)
+	seqNcanAcc=c(spliseqAcc[1:18],spliseqAcc[21:23])
+	sc=rep(0,9)
+	sc[1]=me2x3acc1[hashseq(seqNcanAcc[1:7]),1]
+	sc[2]=me2x3acc2[hashseq(seqNcanAcc[8:14]),1]
+	sc[3]=me2x3acc3[hashseq(seqNcanAcc[15:21]),1]
+	sc[4]=me2x3acc4[hashseq(seqNcanAcc[5:11]),1]
+	sc[5]=me2x3acc5[hashseq(seqNcanAcc[12:18]),1]
+	sc[6]=me2x3acc6[hashseq(seqNcanAcc[5:7]),1]
+	sc[7]=me2x3acc7[hashseq(seqNcanAcc[8:11]),1]
+	sc[8]=me2x3acc8[hashseq(seqNcanAcc[12:14]),1]
+	sc[9]=me2x3acc9[hashseq(seqNcanAcc[15:18]),1]
+	scoreNcan=(sc[1] * sc[2] * sc[3] * sc[4] * sc[5]) /
+		(sc[6] * sc[7] * sc[8] * sc[9])
+	MESscoreAcc <<- log(scoreNcan*valueCanAcc)/log(2)
+}
+
+getMES <- function(sstype,seqCon){
+	if(sstype=="Acc"){
+		scoreMES = MESacceptor(seqCon)
+	}else{
+		if(substr(as.vector(seqCon),4,5)=="GT"){
+			scoreMES = MESdonor(seqCon)
+		}else{
+			scoreMES = 0
+		}
+	}
+	return(scoreMES)
+}
+
+SSFdonGT <- function(SeqDonGT){
+	for(j in 1:9){
+		n=substr(as.vector(SeqDonGT),j,j)
+		i_score[j] = ref_score_GT[n,j]
+	}
+	SSFdonScoreGT <<- ((sum(i_score)-mint_GT)/(maxt_GT-mint_GT))*100
+}
+
+SSFdonGC <- function(SeqDonGC){
+	for(j in 1:9){
+		n=substr(as.vector(SeqDonGC),j,j)
+		i_score[j] = ref_score_GC[n,j]
+	}
+	SSFdonScoreGC <<- ((sum(i_score)-mint_GC)/(maxt_GC-mint_GC))*100
+}
+
+SSFacc <- function(SeqAcc1,SeqAcc2){
+	if(regexpr(pattern="AG",SeqAcc1,fixed=T)>=1){
+		SSFaccScore <<- 0
+	}else{
+		for(l in 1:10){
+			n=substr(SeqAcc1,l,l)
+			i_score1[l]=ref_score_AG[n,l]
+		}
+
+		for(m in 1:4){
+			n=substr(SeqAcc2,m ,m )
+			i_score2[m]=ref_score_AG[n,(m+11) ]
+		}
+		score1=i_score1[order(i_score1,decreasing=T)]
+		score1=score1[1:8]
+		SSFaccScore <<- ((((sum(score1)-mint1)/(maxt1-mint1)) + ((sum(i_score2)-mint2)/(maxt2-mint2)))/2)*100
+	}
+}
+
+getSSF <- function(sstype,seqCon){
+	if (sstype=="Acc"){
+		seqSSFadj=substr(seqCon,7,21)
+		nEch1=substr(as.vector(seqSSFadj),1,10)
+		nEch2=substr(as.vector(seqSSFadj),12,15)
+		SSF = SSFacc(nEch1,nEch2)
+
+	}else{
+		if(substr(as.vector(seqCon),4,5)=="GC"){
+			SSF = SSFdonGT(seqCon)
+		}else{
+			SSF = SSFdonGT(seqCon)
+		}
+	}
+	return(SSF)
+}
+
+getESRscore <- function(sstype,seq){
+	ESRscore=NULL
+	if(sstype=="Acc"){
+		for (i in indAcc){
+			motif = substr(seq,i,i+5)
+			if(motif%in%ESRmotif & motif%in%ESRmotif){
+				if(i<12){
+					ESRscore = c(ESRscore,LEIsc_valuesWA[motif])
+				}else if (i<63){
+					ESRscore = c(ESRscore,LEIsc_valuesHA[motif])
+				}else {
+					ESRscore = c(ESRscore,LEIsc_valuesHM[motif])
+				}
+			}
+		}
+	}else{
+		for (i in indDon){
+			motif = substr(seq,i,i+5)
+			if(motif%in%ESRmotif & motif%in%ESRmotif){
+				if(i<29){
+					ESRscore = c(ESRscore,LEIsc_valuesHM[motif])
+				}else if (i<75){
+					ESRscore = c(ESRscore,LEIsc_valuesHD[motif])
+				}else {
+					ESRscore = c(ESRscore,LEIsc_valuesWD[motif])
+				}
+			}
+		}
+	}
+	if(is.null(ESRscore)){
+		ESRscoreFinal = 0
+	}else{
+		ESRscoreFinal = mean(ESRscore)
+	}
+return(ESRscoreFinal)
+}
+
+getScore <- function(sstype,seq,seqCon){
+	MES = getMES(sstype,seqCon)
+	SSF = getSSF(sstype,seqCon)
+	ESR = getESRscore(sstype,seq)
+	result <<-list(MES,SSF,ESR)
+}
+
+getProbaModel <- function(sstype, MES, SSF, ESR){
+	if(sstype=="Don"){
+		proba = exp(-1.170e+01 + SSF*(5.652e-02 - 1.770e-02) + MES*(4.547e-01 + 6.000e-02) + ESR*(7.005e+00 + 1.239e-01) + 1.756e+00)/
+			(1+exp(-1.170e+01 + SSF*(5.652e-02 - 1.770e-02) + MES*(4.547e-01 + 6.000e-02) + ESR*(7.005e+00 + 1.239e-01) + 1.756e+00))
+	}else{
+		proba = exp(-1.170e+01 + SSF*(5.652e-02) + MES*(4.547e-01) + ESR*(7.005e+00))/
+			(1+exp(-1.170e+01 + SSF*(5.652e-02) + MES*(4.547e-01) + ESR*(7.005e+00)))
+	}
+	return(proba)
+}
+
+getSeqToStudyWTAcc <- function(chr, sens, posAccPhy){
+	if(sens=="+"){
+		start=posAccPhy-19
+		end=posAccPhy+100
+		seqPhysioAcc <- getSequencePhysio (genome,sens,chr,start,end)
+	}else if(sens=="-"){
+		start=posAccPhy+20
+		end=posAccPhy-99
+		seqPhysioAcc <- getSequencePhysio (genome,sens,chr,end,start)
+	}
+	seqConsAccPhyNew <<- substr(seqPhysioAcc,1,23)
+	seqExonAccPhyNew <<- substr(seqPhysioAcc,21,nchar(seqPhysioAcc))
+}
+
+getSeqToStudyWTDon <- function(chr, sens, posDonPhy){
+	if(sens=="+"){
+		start=posDonPhy-99
+		end=posDonPhy+6
+		seqPhysioDon <<- getSequencePhysio (genome,sens,chr,start,end)
+	}else if(sens=="-"){
+		start=posDonPhy+100
+		end=posDonPhy-5
+		seqPhysioDon <<- getSequencePhysio (genome,sens,chr,end,start)
+	}
+		seqConsDonPhyNew <<- substr(seqPhysioDon,98,nchar(seqPhysioDon))
+		seqExonDonPhyNew <<- substr(seqPhysioDon,1,100)
+}
+
+getSplitTableSeq <- function(varName, chr, varPos, sens, seqPhysio, seqMutated, posDon, posAcc, nearestPosAll, varType){
+
+	relPosAccPhy = as.numeric(gregexpr("AG",seqPhysio)[[1]])
+	relPosDonPhy = as.numeric(gregexpr("GT",seqPhysio)[[1]])
+	relPosAccMut = as.numeric(gregexpr("AG",seqMutated)[[1]])
+	relPosDonMut = as.numeric(gregexpr("GT",seqMutated)[[1]])
+
+	relPosAccPhyFilt = relPosAccPhy[relPosAccPhy >= 115 & relPosAccPhy <= 185]
+	relPosDonPhyFilt = relPosDonPhy[relPosDonPhy >= 130 & relPosDonPhy <= 170]
+	relPosAccMutFilt = relPosAccMut[relPosAccMut >= 115 & relPosAccMut <= 185]
+	relPosDonMutFilt = relPosDonMut[relPosDonMut >= 130 & relPosDonMut <= 170]
+
+	seqConsAccPhy = substr(rep(seqPhysio,length(relPosAccPhyFilt)),relPosAccPhyFilt-18,relPosAccPhyFilt+4)
+	seqConsDonPhy = substr(rep(seqPhysio,length(relPosDonPhyFilt)),relPosDonPhyFilt-3,relPosDonPhyFilt+5)
+	seqConsAccMut = substr(rep(seqMutated,length(relPosAccMutFilt)),relPosAccMutFilt-18,relPosAccMutFilt+4)
+	seqConsDonMut = substr(rep(seqMutated,length(relPosDonMutFilt)),relPosDonMutFilt-3,relPosDonMutFilt+5)
+
+	seqExonAccPhy = substr(rep(seqPhysio,length(relPosAccPhyFilt)),relPosAccPhyFilt+2,relPosAccPhyFilt+101)
+	seqExonDonPhy = substr(rep(seqPhysio,length(relPosDonPhyFilt)),relPosDonPhyFilt-100,relPosDonPhyFilt-1)
+	seqExonAccMut = substr(rep(seqMutated,length(relPosAccMutFilt)),relPosAccMutFilt+2,relPosAccMutFilt+101)
+	seqExonDonMut = substr(rep(seqMutated,length(relPosDonMutFilt)),relPosDonMutFilt-100,relPosDonMutFilt-1)
+
+	if(sens == "+"){
+		PosAccPhy = varPos + (relPosAccPhyFilt-150)
+		PosDonPhy = varPos + (relPosDonPhyFilt-152)
+		PosAccMut = varPos + (relPosAccMutFilt-150)
+		PosDonMut = varPos + (relPosDonMutFilt-152)
+		if(varType!="substitution"){
+			if(varType=="del"){
+				PosAccMut[PosAccMut>varPos] = PosAccMut[PosAccMut>varPos] + nbDel
+				PosDonMut[PosDonMut>varPos] = PosDonMut[PosDonMut>varPos] + nbDel
+			}else if(varType=="ins" | varType=="dup"){
+				PosAccMut[PosAccMut>varPos] = PosAccMut[PosAccMut>varPos] - nbIns
+				PosDonMut[PosDonMut>varPos] = PosDonMut[PosDonMut>varPos] - nbIns
+			}else if(varType=="delins"){
+				PosAccMut[PosAccMut>varPos] = PosAccMut[PosAccMut>varPos] - (nbIns - nbDel)
+				PosDonMut[PosDonMut>varPos] = PosDonMut[PosDonMut>varPos] - (nbIns - nbDel)
+			}
+		}
+	}else{
+		PosAccPhy = varPos - (relPosAccPhyFilt-149)
+		PosDonPhy = varPos - (relPosDonPhyFilt-151)
+		PosAccMut = varPos - (relPosAccMutFilt-149)
+		PosDonMut = varPos - (relPosDonMutFilt-151)
+		if(varType!="substitution"){
+			if(varType=="del"){
+				PosAccMut[PosAccMut<varPos] = PosAccMut[PosAccMut<varPos] - nbDel
+				PosDonMut[PosDonMut<varPos] = PosDonMut[PosDonMut<varPos] - nbDel
+			}else if(varType=="ins" | varType=="dup"){
+				PosAccMut[PosAccMut<varPos] = PosAccMut[PosAccMut<varPos] + nbIns
+				PosDonMut[PosDonMut<varPos] = PosDonMut[PosDonMut<varPos] + nbIns
+			}else if(varType=="delins"){
+				PosAccMut[PosAccMut<varPos] = PosAccMut[PosAccMut<varPos] + (nbIns - nbDel)
+				PosDonMut[PosDonMut<varPos] = PosDonMut[PosDonMut<varPos] + (nbIns - nbDel)
+			}
+		}
+	}
+	tmpTableSeq = data.frame(var = rep(varName,length(c(PosAccPhy,PosDonPhy,PosAccMut,PosDonMut))),
+					chr = rep(chr,length(c(PosAccPhy,PosDonPhy,PosAccMut,PosDonMut))),
+					relPos = c(relPosAccPhyFilt,relPosDonPhyFilt,relPosAccMutFilt,relPosDonMutFilt),
+					pos = c(PosAccPhy,PosDonPhy,PosAccMut,PosDonMut),
+					seqCons = c(seqConsAccPhy,seqConsDonPhy,seqConsAccMut,seqConsDonMut),
+					seqExon = c(seqExonAccPhy,seqExonDonPhy,seqExonAccMut,seqExonDonMut),
+					seqType = c(rep("WT",length(c(PosAccPhy,PosDonPhy))),rep("Mut",length(c(PosAccMut,PosDonMut)))),
+					sstype = c(rep("Acc",length(PosAccPhy)),rep("Don",length(PosDonPhy)),rep("Acc",length(PosAccMut)),rep("Don",length(PosDonMut)))
+					)
+	tmpTableSeq$seqCons = as.character(tmpTableSeq$seqCons)
+	tmpTableSeq$seqExon = as.character(tmpTableSeq$seqExon)
+	tmpTableSeq$Physio = "No"
+	tmpTableSeq$Physio[which(tmpTableSeq$pos%in%posAcc & tmpTableSeq$sstype=="Acc")] = "Yes"
+	tmpTableSeq$Physio[which(tmpTableSeq$pos%in%posDon & tmpTableSeq$sstype=="Don")] = "Yes"
+	if(nrow(tmpTableSeq[tmpTableSeq$Physio=="Yes" & tmpTableSeq$seqType=="WT",])==1){
+		SSphy = tmpTableSeq$sstype[tmpTableSeq$Physio=="Yes" & tmpTableSeq$seqType=="WT"]
+		tmpTableSeq = tmpTableSeq[tmpTableSeq$sstype==SSphy,]
+	}
+
+	if(length(nearestPosAll)==2){
+		if(length(which(tmpTableSeq$sstype=="Don"))>0){
+			if(length(which(tmpTableSeq$pos==nearestPosAll[1] & tmpTableSeq$sstype=="Don"))==0){
+				getSeqToStudyWTDon(chr, sens, posDonPhy = nearestPosAll[1])
+				tmpTableSeq = rbind(tmpTableSeq,c(varName,chr,NA,nearestPosAll[1],as.character(seqConsDonPhyNew),as.character(seqExonDonPhyNew),"WT","Don","Yes"))
+			}
+		}
+		if(length(which(tmpTableSeq$sstype=="Acc"))>0){
+			if(length(which(tmpTableSeq$pos==nearestPosAll[2] & tmpTableSeq$sstype=="Acc"))==0){
+				getSeqToStudyWTAcc(chr, sens, posAccPhy = nearestPosAll[2])
+				tmpTableSeq = rbind(tmpTableSeq,c(varName[1],chr[1],NA,nearestPosAll[2],as.character(seqConsAccPhyNew),as.character(seqExonAccPhyNew),"WT","Acc","Yes"))
+			}
+		}
+	}
+	if(nrow(tmpTableSeq[tmpTableSeq$Physio=="Yes",])!=0){
+		tmpTableSeq = tmpTableSeq[!(tmpTableSeq$pos%in%tmpTableSeq$pos[tmpTableSeq$Physio=="Yes"] & tmpTableSeq$Physio!="Yes"),]
+	}
+	tmpScore = mapply(getScore, tmpTableSeq$sstype, as.character(tmpTableSeq$seqExon), as.character(tmpTableSeq$seqCons))
+
+	tmpTableSeq$MES = unlist(tmpScore[1,])
+	tmpTableSeq$SSF = unlist(tmpScore[2,])
+	tmpTableSeq$ESR = unlist(tmpScore[3,])
+
+	tmpProba = mapply(getProbaModel, tmpTableSeq$sstype, tmpTableSeq$MES, tmpTableSeq$SSF , tmpTableSeq$ESR)
+	tmpTableSeq$proba = as.numeric(unlist(tmpProba))
+	tmpTableSeq$proba[tmpTableSeq$proba<0]=0
+	tmpTableSeq$proba[tmpTableSeq$proba>1]=1
+
+	tmpTableSeq$classProba = "No"
+	tmpTableSeq$classProba[tmpTableSeq$proba >= 0.00388264838136624] = "Yes"
+	tmp = merge(tmpTableSeq[tmpTableSeq$seqType=="WT",c("sstype","pos","proba","Physio")],tmpTableSeq[tmpTableSeq$seqType=="Mut",c("sstype","pos","proba","Physio")],
+					by.x = c("sstype","pos"),by.y = c("sstype","pos"),all.x=F,all.y=T)
+	tmp$proba.x[is.na(tmp$proba.x)]=0
+	tmp$Physio.x[is.na(tmp$Physio.x)] = "No"
+
+	tmp = tmp[order(tmp$proba.y,decreasing=T),]
+	tmp = tmp[!duplicated(tmp$pos),]
+	if(length(which(tmpTableSeq$seqType=="Mut" & tmpTableSeq$pos%in%tmp$pos[tmp$proba.x>=tmp$proba.y & tmp$Physio.x!="Yes"]))>0){
+		tmpTableSeq = tmpTableSeq[-which(tmpTableSeq$seqType=="Mut" & tmpTableSeq$pos%in%tmp$pos[tmp$proba.x>=tmp$proba.y & tmp$Physio.x!="Yes"]),]
+	}
+	return(tmpTableSeq)
+}
+
+getDeltaESRseq <- function(SstypePhy, distSS, seqPhysio, seqMutated){
+	if(abs(distSS)>120){
+		ESRscore <<- NA
+	}else{
+		seqESRwt = substr(seqPhysio,146,156)
+		seqESRmut = substr(seqMutated,146,156)
+		ESRscoreMut=NULL
+		ESRscoreWT=NULL
+		j=1
+		if(SstypePhy=="acceptor"){
+			rangeToCheck = (distSS-5):(distSS)
+			if(min(rangeToCheck)<=0){
+				rangeToCheck = 1:distSS
+				seqESRwt = substr(seqESRwt,7-distSS,11)
+				seqESRmut = substr(seqESRmut,7-distSS,11)
+			}
+			for (i in rangeToCheck){
+				motifWT = substr(seqESRwt,j,j+5)
+				motifMUT = substr(seqESRmut,j,j+5)
+				j = j +1
+				if(motifWT%in%ESRmotif){
+					ESRscoreWT = c(ESRscoreWT,ESRlistScore[motifWT])
+				}
+				if(motifMUT%in%ESRmotif){
+					ESRscoreMut = c(ESRscoreMut,ESRlistScore[motifMUT])
+				}
+			}
+		}else{
+			rangeToCheck = (distSS):(distSS+5)
+			if(max(rangeToCheck)>=0){
+				rangeToCheck = distSS:(-1)
+				seqESRwt = substr(seqESRwt,1,11-(6+distSS))
+				seqESRmut = substr(seqESRmut,1,11-(6+distSS))
+			}
+			for (i in rangeToCheck){
+				motifWT = substr(seqESRwt,j,j+5)
+				motifMUT = substr(seqESRmut,j,j+5)
+				j = j +1
+				if(motifWT%in%ESRmotif){
+					ESRscoreWT = c(ESRscoreWT,ESRlistScore[motifWT])
+				}
+				if(motifMUT%in%ESRmotif){
+					ESRscoreMut = c(ESRscoreMut,ESRlistScore[motifMUT])
+				}
+			}
+		}
+		ESRscore = sum(ESRscoreMut) - sum(ESRscoreWT)
+	}
+	return(ESRscore)
+}
+
+getSeqCons <- function(SstypePhy, distSS, seq, varType, varPos, ntChange){
+	if (varType=="del"){
+		nbDel <- abs(varPos[1]-varPos[2])+1
+		if(SstypePhy=="acceptor"){
+			if(distSS<0){
+				if(nbDel>abs(distSS)){
+					seqCons = substr(seq, 131, 153)
+				}else{
+					seqCons = substr(seq, 150-(19+distSS+nbDel), 150+(3-(distSS+nbDel)))
+				}
+			}else{
+				seqCons = substr(seq, 151-(19+distSS), 151+(3-distSS))
+			}
+		}else{
+			if(distSS<0){
+				if(nbDel>abs(distSS)){
+					seqCons = substr(seq, 148, 156)
+				}else{
+					seqCons = substr(seq, 150-(2+distSS+nbDel), 150+(6-(distSS+nbDel)))
+				}
+			}else{
+				seqCons = substr(seq, 151-(2+distSS), 151+(6-distSS))
+			}
+		}
+	}else if (varType=="dup" | varType=="ins"){
+		if (varType=="ins"){
+			nbIns <- nchar(gsub("ins", "", ntChange))
+		}else{
+			nbIns <- abs(varPos[1]-varPos[2])+1
+		}
+		if(SstypePhy=="acceptor"){
+			if(distSS<0){
+				seqCons = substr(seq, 150-(19+distSS) + nbIns, 150+(3-distSS) + nbIns)
+			}else{
+				seqCons = substr(seq, 151-(19+distSS), 151+(3-distSS))
+			}
+		}else{
+			if(distSS<0){
+				seqCons = substr(seq, 150-(2+distSS) + nbIns, 150+(6-distSS) + nbIns)
+			}else{
+				seqCons = substr(seq, 151-(2+distSS), 151+(6-distSS))
+			}
+		}
+	}else if (varType=="delins"){
+		nbDel <- abs(varPos[1]-varPos[2])+1
+		nbIns <- nchar(gsub("delins", "", ntChange))
+		if(SstypePhy=="acceptor"){
+			if(distSS<0){
+				if(nbDel>abs(distSS)){
+					seqCons = substr(seq, 131, 153)
+				}else{
+					seqCons = substr(seq, 150-(19+distSS) + (nbIns-nbDel), 150+(3-distSS) + (nbIns-nbDel))
+				}
+			}else{
+				seqCons = substr(seq, 151-(19+distSS), 151+(3-distSS))
+			}
+		}else{
+			if(distSS<0){
+				if(nbDel>abs(distSS)){
+					seqCons = substr(seq, 148, 156)
+				}else{
+					seqCons = substr(seq, 150-(2+distSS) + (nbIns-nbDel), 150+(6-distSS) + (nbIns-nbDel))
+				}
+			}else{
+				seqCons = substr(seq, 151-(2+distSS), 151+(6-distSS))
+			}
+		}
+	}else{
+		if(SstypePhy=="acceptor"){
+			if(distSS<0){
+				seqCons = substr(seq, 150-(19+distSS), 150+(3-distSS))
+			}else{
+				seqCons = substr(seq, 151-(19+distSS), 151+(3-distSS))
+			}
+		}else{
+			if(distSS<0){
+				seqCons = substr(seq, 150-(2+distSS), 150+(6-distSS))
+			}else{
+				seqCons = substr(seq, 151-(2+distSS), 151+(6-distSS))
+			}
+		}
+	}
+	return(seqCons)
+}
+
+getSPiCE <- function(SstypePhy, seqConsWT, seqConsMut){
+	SSFwt = getSSF(paste(toupper(substr(SstypePhy,1,1)),substr(SstypePhy,2,3),sep=""),seqConsWT)
+	SSFmut = getSSF(paste(toupper(substr(SstypePhy,1,1)),substr(SstypePhy,2,3),sep=""),seqConsMut)
+	MESwt = getMES(paste(toupper(substr(SstypePhy,1,1)),substr(SstypePhy,2,3),sep=""),seqConsWT)
+	MESmut = getMES(paste(toupper(substr(SstypePhy,1,1)),substr(SstypePhy,2,3),sep=""),seqConsMut)
+	if (MESwt==0){
+		deltaMES=0
+	}else{
+		deltaMES = (MESmut-MESwt)/MESwt
+	}
+	if (SSFwt==0){
+		deltaSSF=0
+	}else{
+		deltaSSF = (SSFmut-SSFwt)/SSFwt
+	}
+	SPiCEproba <<- round(exp(-3.59-8.21*round(deltaMES,3)-32.30*round(deltaSSF,3))/(1+exp(-3.59-8.21*round(deltaMES,3)-32.30*round(deltaSSF,3))),5)
+	if(SPiCEproba<0.115){
+		SPiCEinter_2thr <<- "low"
+	}else if(SPiCEproba>0.749){
+		SPiCEinter_2thr <<- "high"
+	}else{
+		SPiCEinter_2thr <<- "medium"
+	}
+}
+
+getDeltaMES <- function(SstypePhy, seqConsWT, seqConsMut){
+	MESwt = getMES(paste(toupper(substr(SstypePhy,1,1)),substr(SstypePhy,2,3),sep=""),seqConsWT)
+	MESmut = getMES(paste(toupper(substr(SstypePhy,1,1)),substr(SstypePhy,2,3),sep=""),seqConsMut)
+	if (MESwt==0){
+		deltaMES=0
+	}else{
+		deltaMES = (MESmut-MESwt)/MESwt
+	}
+	return(deltaMES)
+}
+
+getBPParea <- function(varPos,transcript,genome){
+	if(genome=="hg19"){
+		dataBPannot = dataBPannot19
+	}else{
+		dataBPannot = dataBPannot38
+	}
+
+	tmpAnnotBP = dataBPannot[dataBPannot$transcrit==transcript,]
+	if(nrow(tmpAnnotBP)==0){
+		mutInPBareaBPP = NA
+	}else{
+		if(length(varPos)==1){
+			if(nrow(tmpAnnotBP[tmpAnnotBP$start<=varPos & tmpAnnotBP$end>=varPos,])==1){
+				posBP = tmpAnnotBP[tmpAnnotBP$start<=varPos & tmpAnnotBP$end>=varPos,"posBP"]
+				distToAcc = tmpAnnotBP[tmpAnnotBP$start<=varPos & tmpAnnotBP$end>=varPos,"distToAcc"]
+				score = tmpAnnotBP[tmpAnnotBP$start<=varPos & tmpAnnotBP$end>=varPos,"score"]
+				mutInPBareaBPP = paste("Yes, g.",posBP," (",distToAcc,"): ",round(score,3), sep = "")
+			}else{
+				mutInPBareaBPP = "No"
+			}
+		}else if(length(varPos)==2) {
+			if(nrow(tmpAnnotBP[(tmpAnnotBP$start<=varPos[1] & tmpAnnotBP$end>=varPos[1]) |
+								(tmpAnnotBP$start<=varPos[2] & tmpAnnotBP$end>=varPos[2]) |
+								(tmpAnnotBP$start>varPos[1] & tmpAnnotBP$end<varPos[2]),])==1){
+				posBP = tmpAnnotBP[(tmpAnnotBP$start<=varPos[1] & tmpAnnotBP$end>=varPos[1]) |
+								(tmpAnnotBP$start<=varPos[2] & tmpAnnotBP$end>=varPos[2]) |
+								(tmpAnnotBP$start>varPos[1] & tmpAnnotBP$end<varPos[2]),"posBP"]
+				distToAcc = tmpAnnotBP[(tmpAnnotBP$start<=varPos[1] & tmpAnnotBP$end>=varPos[1]) |
+								(tmpAnnotBP$start<=varPos[2] & tmpAnnotBP$end>=varPos[2]) |
+								(tmpAnnotBP$start>varPos[1] & tmpAnnotBP$end<varPos[2]),"distToAcc"]
+				score = tmpAnnotBP[(tmpAnnotBP$start<=varPos[1] & tmpAnnotBP$end>=varPos[1]) |
+								(tmpAnnotBP$start<=varPos[2] & tmpAnnotBP$end>=varPos[2]) |
+								(tmpAnnotBP$start>varPos[1] & tmpAnnotBP$end<varPos[2]),"score"]
+				mutInPBareaBPP = paste("Yes, g.",posBP," (",distToAcc,"): ",round(score,3), sep = "")
+			}else{
+				mutInPBareaBPP = "No"
+			}
+		}
+	}
+	return(mutInPBareaBPP)
+}
+
+getMutInfo <- function(mutInput){
+	if(length(grep("delins",mutInput ))>0){
+		varPos = unlist(strsplit(mutInput,"delins"))[1]
+		ntChange = paste("delins",unlist(strsplit(mutInput,"delins"))[2],sep="")
+	}else if (length(grep("del",mutInput ))>0){
+		varPos = unlist(strsplit(mutInput,"del"))[1]
+		ntChange = "del"
+	}else if(length(grep("ins",mutInput ))>0){
+		varPos = unlist(strsplit(mutInput,"ins"))[1]
+		ntChange = paste("ins",unlist(strsplit(mutInput,"ins"))[2],sep="")
+	}else if(length(grep("dup",mutInput ))>0){
+		varPos = unlist(strsplit(mutInput,"dup"))[1]
+		ntChange = "dup"
+	}else if(length(grep(">", mutInput, fixed = TRUE))>0){
+		varPos = substr(mutInput,1,nchar(mutInput)-3)
+		ntChange = substr(mutInput,nchar(mutInput)-2,nchar(mutInput))
+	}else{
+		print("Error of mut annotation")
+	}
+	varPos <<- varPos
+	ntChange <<- ntChange
+}
+
+getVariantInfo <- function(varID){
+	varID = as.character(varID)
+	varDecomp=unlist(strsplit(varID,":"))
+	print(varDecomp)
+
+	if(length(varDecomp)!=3 & length(varDecomp)!=2){
+		message("You must import variant as:Transcrit:position(:)nucleotidic change")
+	}else{
+		transcript = varDecomp[1]
+		if(length(grep(".",transcript ))>0){
+			transcript = unlist(strsplit(transcript,".",fixed = T))[1]
+		}
+		if(length(varDecomp)==2){
+			getMutInfo(varDecomp[2])
+		}else{
+			varPos = as.character(varDecomp[2])
+			ntChange = as.character(varDecomp[3])
+		}
+		if(length(grep("delins",ntChange ))>0){
+			varType = "delins"
+			if(length(grep("_",varPos ))>0){
+				varPos = unlist(strsplit(varPos ,"_"))
+				if(length(grep("c.",varPos[1]))>0){
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+					convertcNomenIngNomen(transcript, varPos[1])
+					varPos[1] = gVar
+					convertcNomenIngNomen(transcript, varPos[2])
+					varPos[2] = gVar
+				}else{
+					varPos[1]=substr(varPos[1],3,nchar(varPos[1]))
+				}
+			}else{
+				if(length(grep("c.",varPos[1]))>0){
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+					convertcNomenIngNomen(transcript, varPos[1])
+					varPos = c(gVar,gVar)
+				}else{
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+					varPos = c(varPos,varPos)
+				}
+			}
+		}else if (length(grep("del",ntChange ))>0){
+			varType = "del"
+			if(length(grep("_",varPos ))>0){
+				varPos = unlist(strsplit(varPos ,"_"))
+				if(length(grep("c.",varPos[1]))>0){
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+					convertcNomenIngNomen(transcript, varPos[1])
+					varPos[1] = gVar
+					convertcNomenIngNomen(transcript, varPos[2])
+					varPos[2] = gVar
+				}else{
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+				}
+			}else{
+				if(length(grep("c.",varPos[1]))>0){
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+					convertcNomenIngNomen(transcript, varPos[1])
+					varPos = c(gVar,gVar)
+				}else{
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+					varPos = c(varPos,varPos)
+				}
+			}
+		}else if(length(grep("ins",ntChange ))>0){
+			varType = "ins"
+			if(length(grep("c.",varPos))>0){
+				varPos = substr(varPos,3,nchar(varPos))
+				convertcNomenIngNomen(transcript, varPos)
+				varPos = gVar
+			}else{
+				varPos=substr(varPos,3,nchar(varPos))
+			}
+		}else if(length(grep("dup",ntChange ))>0){
+			varType = "dup"
+			if(length(grep("_",varPos ))>0){
+				varPos = unlist(strsplit(varPos ,"_"))
+				if(length(grep("c.",varPos[1]))>0){
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+					convertcNomenIngNomen(transcript, varPos[1])
+					varPos[1] = gVar
+					convertcNomenIngNomen(transcript, varPos[2])
+					varPos[2] = gVar
+				}else{
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+				}
+			}else{
+				if(length(grep("c.",varPos[1]))>0){
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+					convertcNomenIngNomen(transcript, varPos[1])
+					varPos = c(gVar,gVar)
+				}else{
+					varPos[1] = substr(varPos[1],3,nchar(varPos[1]))
+					varPos = c(varPos,varPos)
+				}
+			}
+		}else{
+			varType = "substitution"
+			if(length(grep("c.",varPos))>0){
+				varPos=substr(varPos,3,nchar(varPos))
+				convertcNomenIngNomen(transcript, varPos)
+				varPos = gVar
+			}else{
+				varPos=substr(varPos,3,nchar(varPos))
+			}
+		}
+	}
+	varID <<- varID
+	varPos <<- as.numeric(varPos)
+	varType <<- varType
+	transcript <<- transcript
+	ntChange <<- ntChange
+}
+
+getGlobaInterpretation <- function(SPiCEinterpret, RegType, deltaMES, mutInPBareaBPP, classProbaMut, distSS, deltaESR){
+	interpretFinal = NULL
+	if(SPiCEinterpret=="high" | SPiCEinterpret=="medium"){
+		interpretFinal = c(interpretFinal,"Alter by SPiCE")
+	}
+	if (length(grep("PolyTC",RegType ))>0 & deltaMES<(-0.15)){
+		interpretFinal = c(interpretFinal,"Alter by MES (Poly TC)")
+	}
+	if (length(grep("BP",RegType ))>0 & mutInPBareaBPP!="No"){
+		interpretFinal = c(interpretFinal,"Alter BP")
+	}
+	if (classProbaMut=="Yes"){
+		if(abs(distSS)>=150 & length(grep("Intron",RegType ))>0) {
+			interpretFinal =c(interpretFinal, "Alter by create Exon")
+		}else{
+			interpretFinal = c(interpretFinal,"Alter by create Cryptic")
+		}
+	}
+	if (length(grep("Exon",RegType ))>0 & abs(distSS)<120){
+		if(deltaESR<(-1.25)) {
+			interpretFinal = c(interpretFinal,"Alter ESR")
+		}else{
+			interpretFinal = c(interpretFinal,"NTR ESR")
+		}
+	}
+	if(is.null(interpretFinal)){
+		interpretFinal = "NTR"
+	}else if (length(interpretFinal)>1){
+		interpretFinal = paste(interpretFinal[interpretFinal!="NTR ESR"], collapse=" + ")
+	}
+	return(interpretFinal)
+}
+
+getPredConfident <- function(interpretFinal, RegType){
+	#proba from SNP + UV analysis
+	probaInter = -1
+	if (length(grep("Exon",RegType ))>0){
+		if(length(grep("Alter by SPiCE",interpretFinal ))>0){
+			probaInter = "80.1 % +/- 6.8 %"
+		}else if (length(grep("Alter ESR",interpretFinal ))>0){
+			probaInter = "24.1 % +/- 4.3 %"
+		}else if (length(grep("Alter by create Cryptic",interpretFinal ))>0){
+			probaInter = "15.9 % +/- 3.0 %"
+		}else if(length(grep("NTR ESR",interpretFinal ))>0){
+			probaInter = "05.5 % +/- 1.4 %"
+		}else if(length(grep("NTR",interpretFinal ))>0){
+			probaInter = "01.1 % +/- 0.8 %"
+		}
+	}else{
+		if(length(grep("Alter by SPiCE",interpretFinal ))>0){
+			probaInter = "92.9 % +/- 2.1 %"
+		}else if (length(grep("Alter by MES",interpretFinal ))>0){
+			probaInter = "75.0 % +/- 12.3 %"
+		}else if (length(grep("Alter BP",interpretFinal ))>0){
+			probaInter = "52.4 % +/- 12.5 %"
+		}else if(length(grep("Alter by create Cryptic",interpretFinal ))>0){
+			probaInter = "08.4 % +/- 2.6 %"
+		}else if(length(grep("Alter by create Exon",interpretFinal ))>0){
+			probaInter = "02.3 % +/- 0.5 %"
+		}else if(length(grep("NTR",interpretFinal ))>0){
+			probaInter = "00.2 % +/- 0.1 %"
+		}
+	}
+	return (probaInter)
+}
+
+getOutput <- function(data,i){
+	getPosSSphysio(transcript)
+	getNearestPos(sens, varPos ,posDon, posAcc)
+
+	start=varPos[1]-150
+	end=varPos[1]+150
+	seqPhysio <<- getSequencePhysio (genome,sens,chr,start,end)
+	getSequenceMutated (varPos, sens, seqPhysio, ntChange, varType, genome, chr)
+	seqPhysio <<- toupper(as.character(seqPhysio))
+	seqMutated <<- toupper(as.character(seqMutated))
+	tmpTableSeq <<- getSplitTableSeq(varID, chr, varPos[1], sens, seqPhysio, seqMutated, posDon, posAcc, nearestPosAll,varType)
+
+	if(as.numeric(gregexpr("Exon",RegType))<0){
+		ESRscore = NA
+	}else{
+		ESRscore = getDeltaESRseq(SstypePhy, distSS, seqPhysio, seqMutated)
+	}
+
+	if(as.numeric(gregexpr("Cons",RegType))<0){
+		seqConsWT = ""
+		seqConsMut = ""
+		SPiCEproba = 0
+		SPiCEinter_2thr = "Outside SPiCE Interpretation"
+	}else{
+		seqConsWT = getSeqCons(SstypePhy, distSS, seqPhysio, varType = "WT", varPos, ntChange)
+		seqConsMut = getSeqCons(SstypePhy, distSS, seqMutated, varType, varPos, ntChange)
+		getSPiCE(SstypePhy, seqConsWT, seqConsMut)
+	}
+	if(as.numeric(gregexpr("PolyTC",RegType))<0){
+		seqConsWT = ""
+		seqConsMut = ""
+		deltaMES = 0
+	}else{
+		seqConsWT = getSeqCons(SstypePhy, distSS, seqPhysio, varType = "WT", varPos, ntChange)
+		seqConsMut = getSeqCons(SstypePhy, distSS, seqMutated, varType, varPos, ntChange)
+		deltaMES = getDeltaMES(SstypePhy, seqConsWT, seqConsMut)
+	}
+	if(as.numeric(gregexpr("BP",RegType))<0){
+		mutInPBareaBPP = "No"
+	}else{
+		mutInPBareaBPP = getBPParea(varPos,transcript,genome)
+	}
+
+	varType <<- varType
+	tmpTableSeqNoPhyMut = tmpTableSeq[tmpTableSeq$Physio!="Yes" & tmpTableSeq$seqType == "Mut",]
+
+	data$chr[i] <<- chr
+	data$strand[i] <<- sens
+	data$gNomen[i] <<- varPos[1]
+	data$NearestSS[i] <<- SstypePhy
+	if(length(varPos)==1){
+		data$distSS[i] <<- distSS
+	}else if(length(varPos)==2){
+		if(distSS[1]==distSS2){
+			data$distSS[i] <<- distSS[1]
+		}else{
+			data$distSS[i] <<- paste(distSS, distSS2,sep="; ")
+		}
+	}else{
+		print("erreur varpos")
+	}
+	data$RegType[i] <<- RegType
+	data$seqPhysio[i] <<- seqPhysio
+	data$seqMutated[i] <<- seqMutated
+	data$SPiCEproba[i] <<- SPiCEproba
+	data$SPiCEinter_2thr[i] <<- SPiCEinter_2thr
+	data$deltaMES[i] <<- deltaMES
+	data$mutInPBarea[i] <<- mutInPBareaBPP
+	data$deltaESRscore[i] <<- ESRscore
+
+	if(nrow(tmpTableSeqNoPhyMut)>0){
+		tmpTableSeqMAXMut = tmpTableSeqNoPhyMut[tmpTableSeqNoPhyMut$proba==max(tmpTableSeqNoPhyMut$proba),]
+		sstypCrypt = tmpTableSeqMAXMut$sstype[1]
+		tmpTableSeqNoPhyWT = tmpTableSeq[tmpTableSeq$Physio!="Yes" & tmpTableSeq$seqType == "WT"& tmpTableSeq$sstype==sstypCrypt,]
+		tmpTableSeqMAXWT = tmpTableSeqNoPhyWT[tmpTableSeqNoPhyWT$proba==max(tmpTableSeqNoPhyWT$proba),]
+
+		tmpTableSeqPhy = tmpTableSeq[tmpTableSeq$Physio=="Yes"& tmpTableSeq$seqType == "WT" & tmpTableSeq$sstype==sstypCrypt,]
+		tmpTableSeqPhyMut = tmpTableSeq[tmpTableSeq$Physio=="Yes"& tmpTableSeq$seqType == "Mut" & tmpTableSeq$sstype==sstypCrypt,]
+
+		getNearestPosCrypt(sens, as.numeric(tmpTableSeqMAXMut$pos) ,posDon, posAcc)
+		data$posCryptMut[i] <<- tmpTableSeqMAXMut$pos
+		data$sstypeCryptMut[i] <<- as.character(tmpTableSeqMAXMut$sstype)
+		data$nearestSStoCrypt[i] <<- SstypePhyCrypt
+		data$nearestPosSStoCrypt[i] <<- nearestPosPhyCrypt
+		data$nearestDistSStoCrypt[i] <<- distSScrypt
+		data$probaCryptMut[i] <<- tmpTableSeqMAXMut$proba
+		data$classProbaCryptMut[i] <<- tmpTableSeqMAXMut$classProba
+		if(nrow(tmpTableSeqMAXWT)>0){
+			data$posCryptWT[i] <<- tmpTableSeqMAXWT$pos[1]
+			data$probaCryptWT[i] <<- tmpTableSeqMAXWT$proba[1]
+			data$classProbaCryptWT[i] <<- tmpTableSeqMAXWT$classProba[1]
+		}
+		if(nrow(tmpTableSeqPhy)>0){
+			data$posSSPhysio[i] <<- tmpTableSeqPhy$pos[1]
+			data$probaSSPhysio[i] <<- tmpTableSeqPhy$proba[1]
+			data$classProbaSSPhysio[i] <<- tmpTableSeqPhy$classProba[1]
+			data$probaSSPhysioMut[i] <<- tmpTableSeqPhy$proba[1]
+			data$classProbaSSPhysioMut[i] <<- tmpTableSeqPhy$classProba[1]
+		}
+		if(nrow(tmpTableSeqPhyMut)>0){
+			data$probaSSPhysioMut[i] <<- tmpTableSeqPhyMut$proba[1]
+			data$classProbaSSPhysioMut[i] <<- tmpTableSeqPhyMut$classProba[1]
+		}
+	}else{
+		data$posCryptMut[i] <<- 0
+		data$sstypeCryptMut[i] <<- "No site"
+		data$nearestSStoCrypt[i] <<- "No site"
+		data$nearestPosSStoCrypt[i] <<- 0
+		data$nearestDistSStoCrypt[i] <<- 0
+		data$probaCryptMut[i] <<- 0
+		data$classProbaCryptMut[i] <<- "No"
+		data$posCryptWT[i] <<- 0
+		data$probaCryptWT[i] <<- 0
+		data$classProbaCryptWT[i] <<- "No"
+		data$posSSPhysio[i] <<- 0
+		data$probaSSPhysio[i] <<- 0
+		data$classProbaSSPhysio[i] <<- "No"
+		data$probaSSPhysioMut[i] <<- 0
+		data$classProbaSSPhysioMut[i] <<- "No"
+	}
+	interpretation <- getGlobaInterpretation(SPiCEinter_2thr, RegType, deltaMES, mutInPBareaBPP, data$classProbaCryptMut[i], distSS[1], ESRscore)
+	data$Interpretation[i] <<- interpretation
+	data$InterConfident[i] <<- getPredConfident(interpretation, RegType)
+}
+
+#launch analysis
+
+T1 <- as.numeric(format(Sys.time(), "%s"))
+
+for (i in 1:nrow(data)){
+	tryCatch({
+		print(i)
+		getVariantInfo(as.character(data$varID[i]))
+		},
+	error=function(cond) {
+		message(paste("Variant caused a error:", data[i,"varID"]))
+		message("Here's the original error message of getVariantInfo function:")
+		message(cond)
+	})
+	tryCatch({
+		getOutput(data,i)
+		},
+	error=function(cond) {
+		message(paste("Variant caused a error:", data[i,"varID"]))
+		message("Here's the original error message of getOutput function:")
+		message(cond)
+	})
+}
+T2 <- as.numeric(format(Sys.time(), "%s"))
+
+print(paste("Runtime:",round((T2 - T1),3),"sec"))
+
+write.table(data,outputFile,sep="\t",dec=".",row.names=F)