Mercurial > repos > proteore > proteore_maps_visualization

comparison 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
comparison
equal deleted inserted replaced
8:ab697ebe0f41 9:9ac0ade20b3f
236 header2 <- str2bool(args$header2) 236 header2 <- str2bool(args$header2)
237 pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col)) 237 pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col))
238 pathways_file = read_file(args$pathways_input,header2) 238 pathways_file = read_file(args$pathways_input,header2)
239 ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE) 239 ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)
240 } 240 }
241 if (args$native_kegg) { ids <- ids[-grep("04215",ids)] } 241 if (args$native_kegg) { ids <- ids[ids != "04215"] }
242 pathways_list <- read_file(args$pathways_list,F) 242 pathways_list <- read_file(args$pathways_list,F)
243 if (!is.null(args$id_list)) { 243 if (!is.null(args$id_list)) {
244 id_list <- get_list_from_cp(args$id_list) 244 id_list <- get_list_from_cp(args$id_list)
245 } 245 }
246 id_type <- tolower(args$id_type) 246 id_type <- tolower(args$id_type)