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RNAseq_1_expr_ballgown.R

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+#!/usr/bin/env Rscript
+# example:
+# Rscript RNAseq_1_ballgown.R -o /home/yuying/rnaseqreport_test -i ./ballgown/ -l FALSE -p test 
+# Rscript RNAseq_1_ballgown.R -o /home/yuying/rnaseqreport_test -i ./ballgown/ 
+
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("ballgown"))
+
+# specify our desired options in a list
+# by default OptionParser will add an help option equivalent to 
+# make_option(c("-h", "--help"), action="store_true", default=FALSE, 
+#               help="Show this help message and exit")
+
+option_list <- list( 
+    make_option(c("-o", "--out_dir"), type="character",default="./",
+        help="The output directory [default ./]"),
+    make_option(c("-i", "--input"),type="character", default=NULL,
+        help="The directory input of expression files. It is output from ballgown software."),
+    make_option(c("-f", "--floor_value"),metavar="number",default=0.01,
+        help="A number to add to each value before log2 transformation to avoid infinite value.[default: 0.01]"),
+    make_option(c("-l", "--log2_norm"), metavar="TRUE", default=TRUE,
+        help="Perform log2 transformation on FPKM value. [default: TRUE]"),
+	make_option(c("-p", "--project_code"), type="character",default="rnaseq",
+        help="Project code, which is used as prefix of output file. [default: rnaseq]")
+		)
+
+# get command line options, if help option encountered print help and exit,
+# otherwise if options not found on command line then set defaults, 
+opt <- parse_args(OptionParser(option_list=option_list))
+
+if (is.null(opt$input)){
+  print_help(opt_parser)
+  stop("At least one argument must be supplied (input file).", call.=FALSE)
+}
+
+#generate FPKM expression profile from ballgown outputs
+geballgown_expr <- ballgown(dataDir =  opt$input ,samplePattern = ".*",meas = "all")
+expr <- gexpr(geballgown_expr)     
+ message("finish ballgown\n")
+
+#remove _1P and FPKM from colnames, _1P is from alicloud app, FPKM is added due to default output of stringtie/ballgown. 
+nam<-colnames(expr)
+nam<-gsub("_1P$","",nam)
+nam<-gsub("^FPKM.","",nam)
+colnames(expr) <- nam
+
+out_dir<-paste(gsub("/$","",opt$out_dir),"/",sep="")
+
+if(opt$log2_norm==TRUE){
+message("start log2 transformation\n")
+
+logexpr<-apply(expr,2,function(x){log2(x+as.numeric(opt$floor_value))})
+logexpr_out<-cbind(rownames(logexpr),round(logexpr,3))
+colnames(logexpr_out)[1]<-"Gene"
+
+message("output log2 expression file\n")
+
+write.table(logexpr_out,file = paste(out_dir,opt$project_code,"_geneexp_log2fpkm_floor0p01_c",ncol(logexpr),"r",nrow(logexpr),"_",Sys.Date(),".txt",sep=""),sep="\t",row.names=F,quote=F)
+}else{ 
+
+#output expression file with fpkm 
+expr<-cbind(rownames(expr),round(expr,3))
+colnames(expr)[1]<-"Gene"
+
+message("output fpkm expression file\n")
+
+write.table(expr,file = paste(out_dir,opt$project_code,"_geneexp_fpkm_c",ncol(expr),"r",nrow(expr),"_",Sys.Date(),".txt",sep=""),sep="\t",row.names=F,quote=F)
+}
+
+
+
+

RNAseq_1_expr_stringtie.R

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+#!/usr/bin/env Rscript
+# example:
+# Rscript RNAseq_1_expr_stringtieout.R 
+#Rscript RNAseq_1_expr_stringtieout.R -o ../ -l FALSE -s samplenames.txt -p 111
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("data.table"))
+
+
+# specify our desired options in a list
+# by default OptionParser will add an help option equivalent to 
+# make_option(c("-h", "--help"), action="store_true", default=FALSE, 
+#               help="Show this help message and exit")
+
+option_list <- list( 
+    make_option(c("-o", "--out_dir"), type="character",default="./",
+        help="The output directory [default ./]"),
+    make_option(c("-i", "--input_dir"),type="character", default="./",
+        help="The directory input of expression files. It is output from stringtie software named as \".gene.abundance.txt\"."),
+    make_option(c("-f", "--floor_value"),metavar="number",default=0.01,
+        help="A number to add to each value before log2 transformation to avoid infinite value.[default: 0.01]"),
+    make_option(c("-l", "--log2_norm"), metavar="TRUE", default=TRUE,
+        help="Perform log2 transformation on FPKM/TPM value. [default: TRUE]"),
+    make_option(c("-s", "--sample_name"),type="character",  default=NULL,
+        help="File in tab-delimited format for sample name if usr want to rename sample name. The input file containing sample name as file name and sample name to be renamed."),
+	make_option(c("-p", "--project_code"), type="character",default="rnaseq",
+        help="Project code, which is used as prefix of output file. [default: rnaseq]")
+		)
+
+# get command line options, if help option encountered print help and exit,
+# otherwise if options not found on command line then set defaults, 
+opt <- parse_args(OptionParser(option_list=option_list))
+
+#modify dir input
+in_dir<-paste(gsub("/$","",opt$input_dir),"/",sep="")
+out_dir<-paste(gsub("/$","",opt$out_dir),"/",sep="")
+
+#read gene.abundance.txt files into 
+if(length(grep("gene.abundance.txt",dir(in_dir)))==0){
+ stop("Cannot find *gene.abundance.txt files in the working folder. Exit!", call.=FALSE)
+}
+
+if(length(grep("gene.abundance.txt",dir(in_dir)))==1){
+ stop("Only one *gene.abundance.txt files in the working folder. Exit!", call.=FALSE)
+}
+
+genefile<-dir(in_dir)[grep("gene.abundance.txt",dir(in_dir))]
+message(paste("Detect ",length(genefile)," files named as *gene.abundance.txt. \nMerging. ",sep=""))
+
+#read first one
+eval(parse(text =paste("a<-fread(\"",genefile[1],"\",header=T,sep=\"\\t\",stringsAsFactors=F,check.names = F,data.table=F)",sep="")))
+atpm<-tapply(a$TPM,as.factor(a$"Gene ID"),mean)
+
+expr_fpkm<-matrix(0,ncol=length(genefile),nrow=length(atpm))
+expr_tpm<-matrix(0,ncol=length(genefile),nrow=length(atpm))
+rownames(expr_fpkm)<-names(atpm)
+rownames(expr_tpm)<-names(atpm)
+#merge gene file
+for (i in 1:length(genefile)){
+eval(parse(text =paste("a<-fread(\"",genefile[i],"\",header=T,sep=\"\\t\",stringsAsFactors=F,check.names = F,data.table=F)",sep="")))
+atpm<-tapply(a$TPM,as.factor(a$"Gene ID"),mean)
+afpkm<-tapply(a$FPKM,as.factor(a$"Gene ID"),mean)
+expr_tpm[,i]<-atpm[match(rownames(expr_tpm),names(atpm))]
+expr_fpkm[,i]<-afpkm[match(rownames(expr_fpkm),names(afpkm))]
+message(paste("Merge ", i, "/",length(genefile)," gene.abundance.txt files ",sep=""))
+}
+
+#colnames
+#remove _1P.gene.abundance.txt from colnames, _1P is from alicloud app
+
+if (is.null(opt$sample_name)){
+samplename<-gsub("_1P.gene.abundance.txt","",genefile)
+message("Sample name is not specified. Using file names instead.")
+}else{
+sample_name<-read.table(opt$sample_name,sep="\t",header=T,stringsAsFactors=F,check.names=F)
+samplename<-gsub("_1P.gene.abundance.txt","",genefile)
+sample_name[,1]<-gsub(".gene.abundance.txt","",sample_name[,1])
+sample_name[,1]<-gsub("_1P$","",sample_name[,1])
+samplename<-sample_name[match(samplename,sample_name[,1]),2]
+}
+colnames(expr_tpm)<-samplename
+colnames(expr_fpkm)<-samplename
+
+
+if(opt$log2_norm==TRUE){
+message("start log2 transformation")
+#tpm
+logexpr_tpm<-apply(expr_tpm,2,function(x){log2(x+as.numeric(opt$floor_value))})
+logexpr_tpm_out<-cbind(rownames(logexpr_tpm),round(logexpr_tpm,3))
+colnames(logexpr_tpm_out)[1]<-"Gene"
+write.table(logexpr_tpm_out,file = paste(out_dir,opt$project_code,"_geneexp_log2TPM.txt",sep=""),sep="\t",row.names=F,quote=F)
+#fpkm
+logexpr_fpkm<-apply(expr_fpkm,2,function(x){log2(x+as.numeric(opt$floor_value))})
+logexpr_fpkm_out<-cbind(rownames(logexpr_fpkm),round(logexpr_fpkm,3))
+colnames(logexpr_fpkm_out)[1]<-"Gene"
+write.table(logexpr_fpkm_out,file = paste(out_dir,opt$project_code,"_geneexp_log2FPKM.txt",sep=""),sep="\t",row.names=F,quote=F)
+message("Write log2 TPM and FPKM expression file.")
+}else{ 
+#output expression file 
+#tpm
+expr_tpm_out<-cbind(rownames(expr_tpm),round(expr_tpm,3))
+colnames(expr_tpm_out)[1]<-"Gene"
+write.table(expr_tpm_out,file = paste(out_dir,opt$project_code,"_geneexp_TPM.txt",sep=""),sep="\t",row.names=F,quote=F)
+#fpkm
+expr_fpkm_out<-cbind(rownames(expr_fpkm),round(expr_fpkm,3))
+colnames(expr_fpkm_out)[1]<-"Gene"
+write.table(expr_fpkm_out,file = paste(out_dir,opt$project_code,"_geneexp_FPKM.txt",sep=""),sep="\t",row.names=F,quote=F)
+message("Write TPM and FPKM expression file.")
+}
+
+
+
+