Mercurial > repos > ebi-gxa > gtf2gene_list

diff gtf2gene.R @ 0:040d4b3a19d5 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 12:05:26 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gtf2gene.R	Wed Apr 03 12:05:26 2019 -0400
@@ -0,0 +1,8 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(require(rtracklayer))
+args <- commandArgs(TRUE)
+
+annotation <- elementMetadata(import( args[1] ))
+genes <- unique(annotation[['gene_id']])
+writeLines(genes[ ! is.na(genes)], con = 'genes.txt')