更新 R/utilities.R, R/gtf.R, R/chr_size.R (5516fd5b) · Commits · Chaos / chaos.tools

R/chr_size.R

+1 −1

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@ chr_size <- function(
		extra = FALSE,
		online = FALSE
		){
		extdata_dir <- "~/.config/chaos.tools"
		extdata_dir <- chaos_info("data_dir")
		chr_size_data <- file.path(extdata_dir,"chr_size.rds")

		if(!file.exists(chr_size_data)){

+39 −17

Original line number	Diff line number	Diff line
		chaos_anno <- function(organism,type = NA){
		if(organism == "human"){
		info <- c(ref = "hg38", anno_v = "v42")
		}else if(organism == "mouse"){
		info <- c(ref = "mm39", anno_v = "vM31")
		}
		if(is.na(type)){
		info
		}else if(type %in% names(info)){
		info[type]
		}
		}

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

		gtf_file <- paste0(
		"~/Reference/",
		chaos_anno(organism,"ref"),
		ref,
		"/annotation/gencode.",
		chaos_anno(organism,"anno_v"),
		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 <- NA}

		if(length(type) == 1){
		if(is.na(type)){
		rds_file <- gsub(".gz",".rds",gtf_file)
		type.str <- NULL
		if(length(type) == 0){
		type_str <- NULL
		}else{
		rds_file <- gsub(".gz",paste0(".",type,".rds"),gtf_file)
		type.str <- type
		type_str <- type.list %>%
		.[. %in% type] %>%
		paste0(collapse = ".") %>%
		paste0(".",.,".rds")
		}
		if(!file.exists(rds_file)){
		r <- import(gtf_file,feature.type = type.str)
		saveRDS(r,rds_file)
		r
		}else{

		rds_file <- paste0(
		chaos_info("data_dir"),
		"/",
		ref,
		".gencode.",
		anno_v,
		".annotation.gtf",
		type_str
		)

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

+11 −29

Original line number	Diff line number	Diff line
		@@ -4,15 +4,17 @@ cumdiff <- function(x)
		}

		chaos_info <- function(
		type
		type = NA
		){
		if(type == "data_dir"){
		"~/.config/chaos.tools"
		}else if(type == "name")
		{
		"chaos.tools"
		n <- c(
		data_dir = "~/.extdata/chaos.tools",
		package_name = "chaos.tools"
		)
		if(is.na(type)){
		n
		}else if(type %in% names(n)){
		n[type]
		}

		}

		chaos_create_dir <- function(
		@@ -21,33 +23,13 @@ chaos_create_dir <- function(
		if(!dir.exists(dir)){dir.create(dir)}
		}

		chaos_anno <- function(organism,type = NA){
		if(organism == "human"){
		ref <- "hg38"
		anno_v <- "v42"
		}else if(organism == "mouse"){
		ref <- "mm39"
		anno_v <- "vM31"
		}
		if(is.na(type)){
		c(ref,anno_v)
		}else if(type == "ref"){
		ref
		}else if(type == "anno_v"){
		anno_v
		}
		}

		update_chaos <- function(
		){
		package_name <- chaos_info("name")

		if(package_name %in% (.packages()))
		{
		if(chaos_info("package") %in% (.packages())){
		detach("package:chaos.tools",unload = T)
		}

		paste0("https://mirrors.sustech.edu.cn/git/fc-ibb105/", package_name,".git") \|>
		paste0("https://mirrors.sustech.edu.cn/git/fc-ibb105/",chaos_info[package_name],".git") \|>
		devtools::install_git()

		library(chaos.tools)