Mercurial > repos > petr-novak > repeat_annotation_pipeline3

view get_gff_part.R @ 4:d7bb42f254a2 draft

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"planemo upload commit fa6d4eb0c804e873b60bb2ba3d0e85646c9cd764"
author petr-novak
date Mon, 14 Mar 2022 10:16:07 +0000
parents ea6a3059a6af
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#!/usr/bin/env Rscript
suppressPackageStartupMessages(library(rtracklayer))
g = import(commandArgs(T)[1])
gd = mcols(g)
col_name=commandArgs(T)[2]
col_value=commandArgs(T)[3]
inc = gd[,col_name] %in% col_value
g_part = sort(sortSeqlevels(g[inc]))
export(g_part, format = 'gff3', commandArgs(T)[4])