modified gtf.R in R (f4f2d324) · Commits · Chaos / chaos.tools

R/gtf.R

+4 −4

Original line number	Diff line number	Diff line
		@@ -35,7 +35,7 @@ gtf <- function(
		paste0(".",.,collapse = "")

		rds_file <- paste0(
		chaos_info("data_dir"),
		c.info("data_dir"),
		"/",
		ref,
		".gencode.",
		@@ -50,7 +50,7 @@ gtf <- function(
		}else{
		if(length(type) == 0){type <- NULL}
		gtf <- BiocIO::import(gtf_file,feature.type = type)
		chaos_create_dir(chaos_info("data_dir"))
		chaos_create_dir(c.info("data_dir"))
		saveRDS(gtf,rds_file,compress = "xz")
		print(paste0(rds_file," saved"))
		gtf
		@@ -63,7 +63,7 @@ txdb <- function(
		ref = NA
		){
		txdb_file <- file.path(
		chaos_info("data_dir"),
		c.info("data_dir"),
		paste0(
		c.basename(gtf_file,".gz"),
		".txdb"
		@@ -73,7 +73,7 @@ txdb <- function(
		if(file.exists(txdb_file)){
		loadDb(txdb_file)
		}else{
		chaos_info("data_dir") \|> chaos_create_dir()
		c.info("data_dir") \|> chaos_create_dir()
		txdb <- gtf_file \|>
		makeTxDbFromGFF(
		dataSource = c.basename(gtf_file,".gz"),