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| Original file line number | Diff line number | Diff line change |
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| featureCounts <- function(files,annot.inbuilt="mm10",annot.ext=NULL,isGTFAnnotationFile=FALSE,GTF.featureType="exon",GTF.attrType="gene_id",GTF.attrType.extra=NULL,chrAliases=NULL,useMetaFeatures=TRUE,allowMultiOverlap=FALSE,minOverlap=1,fracOverlap=0,fracOverlapFeature=0,largestOverlap=FALSE,nonOverlap=NULL,nonOverlapFeature=NULL,readShiftType="upstream",readShiftSize=0,readExtension5=0,readExtension3=0,read2pos=NULL,countMultiMappingReads=TRUE,fraction=FALSE,isLongRead=FALSE,minMQS=0,splitOnly=FALSE,nonSplitOnly=FALSE,primaryOnly=FALSE,ignoreDup=FALSE,strandSpecific=0,juncCounts=FALSE,genome=NULL,isPairedEnd=FALSE,requireBothEndsMapped=FALSE,checkFragLength=FALSE,minFragLength=50,maxFragLength=600,countChimericFragments=TRUE,autosort=TRUE,nthreads=1,byReadGroup=FALSE,reportReads=NULL,reportReadsPath=NULL,maxMOp=10,tmpDir=".",verbose=FALSE, fcounts_clib = NULL) | ||
| { | ||
| flag <- FALSE | ||
| files <- normalizePath(files, mustWork=T) | ||
| if(!is.null(annot.ext) && is.character(annot.ext)) annot.ext <- normalizePath(annot.ext, mustWork=T) | ||
| if(!is.null(chrAliases))chrAliases <- normalizePath(chrAliases, mustWork=T) | ||
| if(!is.null(genome)) genome <- normalizePath(genome, mustWork=T) | ||
| if(!is.null(reportReadsPath)){ | ||
| reportReadsPath <- normalizePath(reportReadsPath, mustWork=T) | ||
| }else reportReadsPath <- ' ' | ||
| strandSpecific<-as.character(strandSpecific) | ||
| strandSpecific<-paste(strandSpecific, collapse=".") | ||
| strandSpecific<-gsub(",", ".", strandSpecific) | ||
|
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||
| if(readShiftSize < 0){ | ||
| stop("The value of the readShiftSize parameter should not be negative.") | ||
| } | ||
|
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||
| if(!(readShiftType %in% c("upstream","downstream","left","right"))){ | ||
| stop("The value of the readShiftType parameter should be one of 'upstream', 'downstream', 'left' and 'right'.") | ||
| } | ||
|
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||
| if(readExtension5 < 0){ | ||
| stop("The value of the readExtension5 parameter should not be negative.") | ||
| } | ||
| if(readExtension3 < 0){ | ||
| stop("The value of the readExtension3 parameter should not be negative.") | ||
| } | ||
|
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| annot.screen.output <- 'R data.frame' | ||
| if(is.null(annot.ext)){ | ||
| switch(tolower(as.character(annot.inbuilt)), | ||
| mm9={ | ||
| ann <- system.file("annot","mm9_RefSeq_exon.txt",package="Rsubread") | ||
| annot.screen.output <- 'inbuilt (mm9)' | ||
| }, | ||
| mm10={ | ||
| ann <- system.file("annot","mm10_RefSeq_exon.txt",package="Rsubread") | ||
| annot.screen.output <- 'inbuilt (mm10)' | ||
| }, | ||
| hg19={ | ||
| ann <- system.file("annot","hg19_RefSeq_exon.txt",package="Rsubread") | ||
| annot.screen.output <- 'inbuilt (hg19)' | ||
| }, | ||
| hg38={ | ||
| ann <- system.file("annot","hg38_RefSeq_exon.txt",package="Rsubread") | ||
| annot.screen.output <- 'inbuilt (hg38)' | ||
| }, | ||
| { | ||
| stop("In-built annotation for ", annot.inbuilt, " is not available.\n") | ||
| } | ||
| ) # end switch | ||
| } | ||
| else{ | ||
| if(is.character(annot.ext)){ | ||
| ann <- annot.ext | ||
| annot.screen.output <- paste0(basename(ann), " (", ifelse(isGTFAnnotationFile, "GTF", "SAF"), ")"); | ||
| } | ||
| else{ | ||
| annot_df <- as.data.frame(annot.ext,stringsAsFactors=FALSE) | ||
| if(sum(c("geneid","chr","start","end", "strand") %in% tolower(colnames(annot_df))) != 5) | ||
| stop("One or more required columns are missing in the provided annotation data. Please refer to help page for annotation format.\n") | ||
| colnames(annot_df) <- tolower(colnames(annot_df)) | ||
| annot_df <- data.frame(geneid=annot_df$geneid,chr=annot_df$chr,start=annot_df$start,end=annot_df$end,strand=annot_df$strand,stringsAsFactors=FALSE) | ||
| annot_df$chr <- as.character(annot_df$chr) | ||
| fout_annot <- file.path(".",paste(".Rsubread_UserProvidedAnnotation_pid",Sys.getpid(),sep="")) | ||
| oldScipen <- options(scipen=999) | ||
| write.table(x=annot_df,file=fout_annot,sep="\t",row.names=FALSE,quote=FALSE) | ||
| options(oldScipen) | ||
| ann <- fout_annot | ||
| flag <- TRUE | ||
| } | ||
| } | ||
|
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| fout <- file.path(".",paste(".Rsubread_featureCounts_pid",Sys.getpid(),sep="")) | ||
|
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| files_C <- paste(files,collapse=";") | ||
|
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| if(nchar(files_C) == 0) stop("No read files provided!") | ||
|
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| genome_C <- genome | ||
| if(is.null(genome)) | ||
| genome_C <- " " | ||
|
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| chrAliases_C <- chrAliases | ||
| if(is.null(chrAliases)) | ||
| chrAliases_C <- " " | ||
|
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| read2pos_C <- read2pos | ||
| if(is.null(read2pos)) read2pos_C <- 0 | ||
|
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| split_C <- 0 | ||
| if(splitOnly) split_C <- 1 | ||
| if(nonSplitOnly) split_C <- 2 | ||
|
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| PE_orientation <- "fr" | ||
|
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| if(is.null(reportReads)) { | ||
| reportReads_C <- 0 | ||
| } else if(reportReads == "CORE") { | ||
| reportReads_C <- 10 | ||
| } else if(reportReads == "SAM") { | ||
| reportReads_C <- 50 | ||
| } else if(reportReads == "BAM") { | ||
| reportReads_C <- 500 | ||
| } else | ||
| stop("Invalid value was provided for reportReads parameter.") | ||
|
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| do_detection_calls <- FALSE | ||
| max_missing_bases_in_read <- -1 | ||
| max_missing_bases_in_feature <- -1 | ||
| GTF.attrType.extra_str <- " " | ||
| if(!is.null(nonOverlap)) max_missing_bases_in_read <- nonOverlap | ||
| if(!is.null(nonOverlapFeature)) max_missing_bases_in_feature <- nonOverlapFeature | ||
| if(!is.null(GTF.attrType.extra))GTF.attrType.extra_str <- paste(GTF.attrType.extra, collapse="\t") | ||
|
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| cmd <- paste("readSummary",ann,files_C,fout,as.numeric(isPairedEnd),minFragLength,maxFragLength,0,as.numeric(allowMultiOverlap),as.numeric(useMetaFeatures),nthreads,as.numeric(isGTFAnnotationFile),strandSpecific,reportReads_C,as.numeric(requireBothEndsMapped),as.numeric(!countChimericFragments),as.numeric(checkFragLength),GTF.featureType,GTF.attrType,minMQS,as.numeric(countMultiMappingReads),chrAliases_C," ",as.numeric(FALSE),14,readExtension5,readExtension3,minOverlap,split_C,read2pos_C," ",as.numeric(ignoreDup),as.numeric(!autosort),as.numeric(fraction),as.numeric(largestOverlap),PE_orientation,as.numeric(juncCounts),genome_C,maxMOp,0,as.numeric(fracOverlap),as.character(tmpDir),"0",as.numeric(byReadGroup),as.numeric(isLongRead),as.numeric(verbose),as.numeric(fracOverlapFeature), as.numeric(do_detection_calls), as.numeric(max_missing_bases_in_read), as.numeric(max_missing_bases_in_feature), as.numeric(primaryOnly), reportReadsPath, GTF.attrType.extra_str, annot.screen.output, readShiftType,readShiftSize ,sep=",") | ||
| n <- length(unlist(strsplit(cmd,","))) | ||
| dyn.load(fcounts_clib) | ||
| C_args <- .C("R_readSummary_wrapper",as.integer(n),as.character(cmd)) | ||
| dyn.unload(fcounts_clib) | ||
|
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| if(file.exists(fout)){ | ||
| x <- read.delim(fout,stringsAsFactors=FALSE) | ||
| colnames(x)[1:6] <- c("GeneID","Chr","Start","End","Strand","Length") | ||
|
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| x_summary <- read.delim(paste(fout,".summary",sep=""), stringsAsFactors=FALSE) | ||
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| if(juncCounts) | ||
| x_jcounts <- read.delim(paste(fout,".jcounts",sep=""), stringsAsFactors=FALSE) | ||
|
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| file.remove(fout) | ||
| file.remove(paste(fout,".summary",sep="")) | ||
|
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| if(juncCounts) | ||
| file.remove(paste(fout,".jcounts",sep="")) | ||
|
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| if(flag) | ||
| file.remove(fout_annot) | ||
|
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| add_attr_numb <- 0 | ||
| if(!is.null(GTF.attrType.extra)) add_attr_numb <- length(GTF.attrType.extra) | ||
| if(ncol(x) <= (6 + add_attr_numb)){ | ||
| stop("No count data were generated.") | ||
| } | ||
|
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| y <- as.matrix(x[,-c(1:(6 + add_attr_numb))]) | ||
| colnames(y) <- colnames(x)[-c(1:(6 + add_attr_numb))] | ||
| rownames(y) <- x$GeneID | ||
|
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| if(juncCounts) | ||
| z <- list(counts=y,counts_junction=x_jcounts,annotation=x[,1:(6 + add_attr_numb)],targets=colnames(y),stat=x_summary) | ||
| else | ||
| z <- list(counts=y,annotation=x[,1:(6 + add_attr_numb)],targets=colnames(y),stat=x_summary) | ||
| z | ||
| }else{ | ||
| stop("No counts were generated.") | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -3,7 +3,7 @@ | |
| # Pipeline to run UMI-seq analysis from fastq to read count tables. | ||
| # Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann | ||
| # Contact: [email protected] or [email protected] | ||
| vers=2.5.3 | ||
| vers=2.5.4 | ||
| currentv=`curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.sh | grep '^vers=' | cut -f2 -d "="` | ||
| if [ "$currentv" != "$vers" ]; then echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------"; fi | ||
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