gff2gtf.R

gff2gtf.R

#!/usr/bin/env Rscript

# Based on https://www.biostars.org/p/45791/#45804
#
# Usage:
#  ./gff2gtf.R genes.gff genes.gtf
#
# Dependencies can be easily installed like:
#  conda create -n gff2gtf bioconductor-rtracklayer
#  conda activate gff2gtf

# Set a working CRAN mirror
local({r <- getOption("repos")
       r["CRAN"] <- "http://cloud.r-project.org" 
       options(repos=r)
})

# Install pacman and rtracklayer if not present
if (!require("pacman")) {
  install.packages("pacman")
}

pacman::p_install(rtracklayer, 
                  try.bioconductor=TRUE, 
                  force=FALSE, 
                  update.bioconductor=TRUE)

library(rtracklayer)

args = commandArgs(trailingOnly=TRUE)

gff_features <- import(args[1])
export(gff_features, args[2], "gtf")