Mercurial > repos > petr-novak > repeat_annotation_pipeline3

view get_gff_part.R @ 11:5366d5ea04bc draft

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planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
author petr-novak
date Fri, 04 Aug 2023 12:35:32 +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])