modified gtf.R in R (0ab056cf) · Commits · Chaos / chaos.tools

R/gtf.R

+6 −1

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

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

		if(is.na(gtf_file)){
		gtf_file <- paste0(
		"~/Reference/",
		ref,
		@@ -25,6 +27,7 @@ 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]
		@@ -49,10 +52,12 @@ gtf <- function(
		)

		if(file.exists(rds_file)){
		print(paste0(rds_file," exists, reading file"))
		readRDS(rds_file)
		}else{
		gtf <- BiocIO::import(gtf_file,feature.type = type)
		saveRDS(gtf,rds_file,compress = "xz")
		print(paste0(rds_file," saved"))
		gtf
		}
		}
		No newline at end of file