From 98c7198959e66e47bb629040175842810144f015 Mon Sep 17 00:00:00 2001 From: raphaelleman Date: Fri, 1 Mar 2019 12:20:14 +0100 Subject: [PATCH] SPiP script v1 --- SPiPv0.2.r | 1755 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 1755 insertions(+) create mode 100644 SPiPv0.2.r 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=(-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 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[PosAccMut0){ + 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[1]) | + (tmpAnnotBP$start<=varPos[2] & tmpAnnotBP$end>=varPos[2]) | + (tmpAnnotBP$start>varPos[1] & tmpAnnotBP$end=varPos[1]) | + (tmpAnnotBP$start<=varPos[2] & tmpAnnotBP$end>=varPos[2]) | + (tmpAnnotBP$start>varPos[1] & tmpAnnotBP$end=varPos[1]) | + (tmpAnnotBP$start<=varPos[2] & tmpAnnotBP$end>=varPos[2]) | + (tmpAnnotBP$start>varPos[1] & tmpAnnotBP$end0){ + 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)