modified gtf.R in R (e74fed4b) · Commits · Chaos / chaos.tools

R/gtf.R

+3 −10

Original line number	Diff line number	Diff line
		@@ -13,13 +13,11 @@ chaos_anno <- function(organism,type = NA){

		gtf <- function(
		organism,
		type = NA,
		gtf_file = NA
		type = NA
		){
		ref <- chaos_anno(organism,"ref")
		anno_v <- chaos_anno(organism,"anno_v")

		if(is.na(gtf_file)){
		gtf_file <- paste0(
		"~/Reference/",
		ref,
		@@ -27,19 +25,14 @@ gtf <- function(
		anno_v,
		".annotation.gtf.gz"
		)
		}

		type.list <- c("gene","transcript","exon","CDS","start_codon","stop_codon","UTR","Selenocysteine")
		type <- type %>% .[. %in% type.list]

		if(length(type) == 0){
		type_str <- NULL
		}else{
		type_str <- type.list %>%
		.[. %in% type] %>%
		paste0(collapse = ".") %>%
		paste0(".",.,".rds")
		}
		c("rds") %>%
		paste0(".",.,collapse = ".")

		rds_file <- paste0(
		chaos_info("data_dir"),