rename gene_biotype->gene_type in GTF (#162)

gagneurlab · Feb 5, 2021 · ff23438 · ff23438
1 parent cfe6dbd
commit ff23438
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/drop/modules/mae-pipeline/MAE/gene_name_mapping.R b/drop/modules/mae-pipeline/MAE/gene_name_mapping.R
@@ -24,6 +24,8 @@ gtf_dt <- import(snakemake@input$gtf) %>% as.data.table
 if (!"gene_name" %in% colnames(gtf_dt)) {
   gtf_dt[gene_name := gene_id]
 }
+if('gene_biotype' %in% colnames(gtf_dt))
+   setnames(gtf_dt, 'gene_biotype', 'gene_type')
 gtf_dt <- gtf_dt[type == "gene", .(seqnames, start, end, strand, gene_id, gene_name, gene_type)]
 
 # make gene_names unique