Mercurial > repos > proteore > proteore_maps_visualization

diff kegg_maps_visualization.R @ 9:9ac0ade20b3f draft

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"planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty"
author proteore
date Wed, 08 Jan 2020 09:03:41 +0000
parents ab697ebe0f41
children a4db9efe1e43
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line diff
--- a/kegg_maps_visualization.R	Mon Jan 06 16:26:09 2020 +0000
+++ b/kegg_maps_visualization.R	Wed Jan 08 09:03:41 2020 +0000
@@ -238,7 +238,7 @@
     pathways_file = read_file(args$pathways_input,header2)
     ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
   }
-  if (args$native_kegg) { ids <- ids[-grep("04215",ids)] }
+  if (args$native_kegg) { ids <- ids[ids != "04215"] }
   pathways_list <- read_file(args$pathways_list,F)
   if (!is.null(args$id_list)) {
     id_list <- get_list_from_cp(args$id_list)