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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| Date: 21 May 2017 | ||
| - First submission |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,188 @@ | ||
| ############## | ||
| ##### analyze input: Rscript test.R in=inputFeqDir txfasta=txFastaFile sqlite=gtfSqlite txanno=txAnnofile out=outputDir params=paramsFn | ||
| inputFeqDir=txFastaFile=gtfSqlite=txAnnofile=outputDir=paramsFn=NA | ||
| #get command information | ||
| args = commandArgs(trailingOnly=TRUE) | ||
| cat("\nNumber of arguments: ",length(args)) | ||
| cat("\nList of arguments: ",args) | ||
| for (i in 1:length(args)){ | ||
| res=unlist(strsplit(args[i],"=")) | ||
| if (res[1]=="in") inputFeqDir=res[2] | ||
| if (res[1]=="txfasta") txFastaFile=res[2] | ||
| if (res[1]=="sqlite") gtfSqlite=res[2] | ||
| if (res[1]=="txanno") txAnnofile=res[2] | ||
| if (res[1]=="params") paramsFn=res[2] | ||
| if (res[1]=="out") outputDir=res[2] | ||
| } | ||
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| #check input information | ||
| validatedCommand=TRUE | ||
| if (is.na(inputFeqDir)){ | ||
| cat("\nThere is no input folder. Stop!") | ||
| validatedCommand=FALSE | ||
| } | ||
| if (is.na(txFastaFile)){ | ||
| cat("\nThere is no transcript fasta file. Stop!") | ||
| validatedCommand=FALSE | ||
| } | ||
| if (is.na(gtfSqlite)){ | ||
| cat("\nThere is no sqlite file. Stop!") | ||
| validatedCommand=FALSE | ||
| } | ||
| if (is.na(txAnnofile)){ | ||
| cat("\nThere is no txAnno file. Stop!") | ||
| validatedCommand=FALSE | ||
| } | ||
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| if (is.na(outputDir)){ | ||
| cat("\n-----") | ||
| cat("\nThere is no output directory from user, the output will be saved into the input directory of fusion equivalence classes.") | ||
| outputDir=inputFeqDir | ||
| }else{ | ||
| if (dir.exists(outputDir)){ | ||
| cat("\nCan not create the output directory. Stop!") | ||
| validatedCommand=FALSE | ||
| }else dir.create(outputDir) | ||
| } | ||
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| if (is.na(paramsFn)){ | ||
| cat("\n-----") | ||
| cat("\nThere is no params file. Default settings will be used.") | ||
| FuSeq.params=list() | ||
| FuSeq.params$readStrands="UN" | ||
| FuSeq.params$chromRef=as.character(c(1:22,"X","Y")) | ||
| FuSeq.params$onlyProteinCodingGenes=TRUE | ||
| FuSeq.params$maxSharedCount=5e-2 | ||
| FuSeq.params$minGeneDist=1e5 | ||
| FuSeq.params$minJunctionDist=1e5 | ||
| FuSeq.params$maxInvertedFusionCount=0.01 | ||
| FuSeq.params$maxMRfusionFc=2 | ||
| FuSeq.params$maxMRfusionNum=2 | ||
| FuSeq.params$sgtMRcount=10 | ||
| FuSeq.params$minMR=2 | ||
| FuSeq.params$minNonDupMR=2 | ||
| FuSeq.params$minSR=1 | ||
| FuSeq.params$minScore=3 | ||
| FuSeq.params$keepRData=FALSE | ||
| FuSeq.params$exportFasta=FALSE | ||
| }else{ | ||
| paramIn=read.table(paramsFn, sep="=", header=FALSE) | ||
| FuSeq.params=list() | ||
| FuSeq.params$readStrands=as.character(paramIn[which(paramIn[,1]=="readStrands"),2]) | ||
| FuSeq.params$chromRef=trimws(unlist(strsplit(as.character(paramIn[which(paramIn[,1]=="chromRef"),2]),","))) | ||
| FuSeq.params$onlyProteinCodingGenes=as.logical(as.character(paramIn[which(paramIn[,1]=="onlyProteinCodingGenes"),2])) | ||
| FuSeq.params$maxSharedCount=as.double(as.character(paramIn[which(paramIn[,1]=="maxSharedCount"),2])) | ||
| FuSeq.params$minGeneDist=as.double(as.character(paramIn[which(paramIn[,1]=="minGeneDist"),2])) | ||
| FuSeq.params$minJunctionDist=as.double(as.character(paramIn[which(paramIn[,1]=="minJunctionDist"),2])) | ||
| FuSeq.params$maxInvertedFusionCount=as.double(as.character(paramIn[which(paramIn[,1]=="maxInvertedFusionCount"),2])) | ||
| FuSeq.params$maxMRfusionFc=as.double(as.character(paramIn[which(paramIn[,1]=="maxMRfusionFc"),2])) | ||
| FuSeq.params$maxMRfusionNum=as.double(as.character(paramIn[which(paramIn[,1]=="maxMRfusionNum"),2])) | ||
| FuSeq.params$sgtMRcount=as.double(as.character(paramIn[which(paramIn[,1]=="sgtMRcount"),2])) | ||
| FuSeq.params$minMR=as.double(as.character(paramIn[which(paramIn[,1]=="minMR"),2])) | ||
| FuSeq.params$minNonDupMR=as.double(as.character(paramIn[which(paramIn[,1]=="minNonDupMR"),2])) | ||
| FuSeq.params$minSR=as.double(as.character(paramIn[which(paramIn[,1]=="minSR"),2])) | ||
| FuSeq.params$minScore=as.double(as.character(paramIn[which(paramIn[,1]=="minScore"),2])) | ||
| FuSeq.params$keepRData=as.logical(as.character(paramIn[which(paramIn[,1]=="keepRData"),2])) | ||
| FuSeq.params$exportFasta=as.logical(as.character(paramIn[which(paramIn[,1]=="exportFasta"),2])) | ||
| } | ||
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| if (validatedCommand){ | ||
| cat("\n-----") | ||
| cat("\nParameter settings:") | ||
| cat("\n readStrands=",FuSeq.params$readStrands) | ||
| cat("\n chromRef="); cat(FuSeq.params$chromRef,sep = ",") | ||
| cat("\n maxSharedCount=",FuSeq.params$maxSharedCount) | ||
| cat("\n onlyProteinCodingGenes=",FuSeq.params$onlyProteinCodingGenes) | ||
| cat("\n minGeneDist=",FuSeq.params$minGeneDist) | ||
| cat("\n minJunctionDist=",FuSeq.params$minJunctionDist) | ||
| cat("\n maxInvertedFusionCount=",FuSeq.params$maxInvertedFusionCount) | ||
| cat("\n maxMRfusionFc=",FuSeq.params$maxMRfusionFc) | ||
| cat("\n maxMRfusionNum=",FuSeq.params$maxMRfusionNum) | ||
| cat("\n sgtMRcount=",FuSeq.params$sgtMRcount) | ||
| cat("\n minMR=",FuSeq.params$minMR) | ||
| cat("\n minNonDupMR=",FuSeq.params$minNonDupMR) | ||
| cat("\n minSR=",FuSeq.params$minSR) | ||
| cat("\n minScore=",FuSeq.params$minScore) | ||
| cat("\n keepRData=",FuSeq.params$keepRData) | ||
| cat("\n exportFasta=",FuSeq.params$exportFasta) | ||
| } | ||
| cat("\n-------------------------\n") | ||
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| if (validatedCommand){ | ||
| #load gtf annotation information | ||
| suppressMessages(library("GenomicFeatures")) | ||
| anntxdb <- loadDb(gtfSqlite) | ||
| load(txAnnofile) | ||
| #load R functions | ||
| source("/path/to/FuSeq_functions.R") | ||
| source("/path/to/processFEQ.R") | ||
| source("/path/to/detectJunctionBreaks.R") | ||
| source("/path/to/doBiologicalFilter.R") | ||
| source("/path/to/processMappedRead.R") | ||
| source("/path/to/processSplitRead.R") | ||
| source("/path/to/postProcessMappedRead.R") | ||
| source("/path/to/postProcessSplitRead.R") | ||
| source("/path/to/integrateFusion.R") | ||
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| inPath=inputFeqDir | ||
| myFusionOut=NULL; | ||
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| FuSeq.MR=processMappedRead(inPath,geneAnno=geneAnno, anntxdb=anntxdb, geeqMap=geeqMap,FuSeq.params=FuSeq.params) | ||
| FuSeq.SR=processSplitRead(inPath,geneAnno=geneAnno, anntxdb=anntxdb, geeqMap=geeqMap,FuSeq.params=FuSeq.params, txFastaFile=txFastaFile) | ||
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| FuSeq.MR.postPro=postProcessMappedRead(inPath, anntxdb, FuSeq.SR, FuSeq.MR, FuSeq.params) | ||
| FuSeq.SR.postPro=postProcessSplitRead(inPath, anntxdb, FuSeq.SR, FuSeq.MR, txFastaFile, FuSeq.params) | ||
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| myFusionFinal.MR=FuSeq.MR.postPro$myFusionFinal | ||
| myFusionFinal.SR=FuSeq.SR.postPro$myFusionFinal | ||
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| fragmentInfo=FuSeq.MR$fragmentInfo | ||
| FuSeq.integration=integrateFusion(myFusionFinal.MR, myFusionFinal.SR, FuSeq.params, fragmentInfo=fragmentInfo, paralog.fc.thres=2.0) | ||
| myFusionFinal=FuSeq.integration$myFusionFinal | ||
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| if (nrow(myFusionFinal)==0){ | ||
| myFusionExport= "# No fusion genes existing" | ||
| write.table(myFusionExport, file=outputDir, col.names=FALSE, row.names = FALSE,quote = FALSE, sep="\t") | ||
| } else{ | ||
| myFusionOut=myFusionFinal | ||
| myFusionOut=myFusionOut[order(myFusionOut$score, decreasing = TRUE),] | ||
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| myFusionExport=myFusionOut[,c("gene5","chrom5p","strand5p","brpos5.start","brpos5.end","gene3","chrom3p","strand3p","brpos3.start","brpos3.end","fusionName","supportRead","score")] | ||
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| colnames(myFusionExport)=c("gene5","chrom5","strand5","brpos5.start","brpos5.end","gene3","chrom3","strand3","brpos3.start","brpos3.end","fusionName","supportRead","score") | ||
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| #Detect extra information here | ||
| myFusionExport$info=rep("",nrow(myFusionExport)) | ||
| myID=unique(c(which(!is.na(myFusionOut$mitoTrans5)),which(!is.na(myFusionOut$mitoTrans3)))) | ||
| myFusionExport$info[myID]=paste(myFusionExport$info[myID],"mitochondrial translation, ",sep="") | ||
| myID=unique(c(which(!is.na(myFusionOut$ribSub5)),which(!is.na(myFusionOut$ribSub3)))) | ||
| myFusionExport$info[myID]=paste(myFusionExport$info[myID],"cytosolic ribosomal subunit, ",sep="") | ||
| myID=unique(c(which(!is.na(myFusionOut$ribonupro5)),which(!is.na(myFusionOut$ribonupro3)))) | ||
| myFusionExport$info[myID]=paste(myFusionExport$info[myID],"ribonucleoprotein, ",sep="") | ||
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| write.table(myFusionExport, file=paste(outputDir,"/fusions.FuSeq",sep=""), col.names=TRUE, row.names = FALSE,quote = FALSE, sep="\t") | ||
| ##### | ||
| #keep all RData | ||
| if (FuSeq.params$keepRData){ | ||
| cat("\n Saving all data of FuSeq process...") | ||
| save(inPath,outputDir, myFusionFinal,myFusionExport,FuSeq.params, FuSeq.MR, FuSeq.SR, FuSeq.MR.postPro, FuSeq.SR.postPro,FuSeq.integration, file=paste(outputDir,"/FuSeq_process.RData",sep="")) | ||
| } | ||
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| ##### Export fasta sequence | ||
| if (FuSeq.params$exportFasta){ | ||
| cat("\n Export supporing read sequences to files...") | ||
| fastaOut=paste(outputDir,"/FuSeq_",sep="") | ||
| exportMappedFusionReads(inPath, readStrands=FuSeq.params$readStrands, fastaOut=fastaOut, junctInfo=FuSeq.MR$junctBr$junctInfo, fusionName=as.character(myFusionFinal$fusionName),fsizeLadder=FuSeq.MR$junctBr$fsizeLadder) | ||
| exportSplitFusionReads(inPath, readStrands=FuSeq.params$readStrands, fastaOut=fastaOut, splitReads=FuSeq.SR$splitReads, fusionName=as.character(myFusionFinal$fusionName)) | ||
| } | ||
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| } | ||
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| cat("\n Done! \n") | ||
| } | ||
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