tx2gene.R

In sarangian/deaRscripts: Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups

#!/usr/bin/env Rscript
suppressMessages(library(rnaseqdea))
suppressMessages(library(optparse))
suppressMessages(library(stringr))
suppressMessages(library(plyranges))
suppressMessages(library(dplyr))
suppressMessages(library(tidyr))
rm(list=ls())                                        # remove all the objects from the R session

option_list <- list( 

make_option(c("-a", "--annoType"),dest="annotation",help="annotation file type gff3 or gtf"),
make_option(c("-p", "--path"), dest="filePath",type="character", default=NULL,help="annotation file file path", metavar="character"),
make_option(c("-o", "--out"), type="character", default=NULL,help="tx2gene file name (.csv)", metavar="character")
)
parser <- OptionParser(usage="usage: %prog [options]",
					   option_list=option_list, 
					   description="Generate tx2gene from gff3 file.",
					   epilogue="Computational Genome Biology Lab, CSIR-IICB, Kolkata 700032")    

 
opt <- parse_args(parser, args=commandArgs(trailingOnly=TRUE), positional_arguments=0)$options

fileType <- opt$annotation
filePath <- opt$filePath
fileOut <- opt$out   


if(fileType=="gff3"){
    tx2gene <- tr2g_gff3(filePath)
    tx2gene$gene <-paste(tx2gene$gene,tx2gene$gene_name, sep = ":")
    tx2g <-paste(tx2gene$transcript,tx2gene$gene,sep=",")
    tx2g <- str_remove_all(tx2g, "rna-")
    tx2g <- str_remove_all(tx2g, "gene-")
    colnames(tx2g) <- NULL
    names(tx2g)[1] <- "TRANSCRIPT"
    names(tx2g)[2] <- "GENE"
    write.table(tx2g,opt$out, sep=",", col.names = TRUE, row.names = FALSE, quote=FALSE)
    }

if(fileType=="gtf"){
    tx2gene <- tr2g_gtf(filePath)
    colnames(tx2gene) <- NULL    
    names(tx2gene)[1] <- "TRANSCRIPT"
    names(tx2gene)[2] <- "GENE"
    write.table(tx2gene,opt$out, sep=",", col.names = TRUE, row.names = FALSE, quote=FALSE)
    }