HicSnake/scripts/calder

#!/usr/bin/env Rscript
###########################################################################
# 该程序修改自 https://github.com/CSOgroup/CALDER2/blob/main/scripts/calder
# 1. 源程序无法正确处理染色体名称不以 chr 为前缀的情况
# 2. 只修改了 cool 格式作为输入文件，hic 格式预计仍然有 bug 未测试
# 3. 如果染色体前缀不一致，无法处理
# 4. 增加了对 mcool 格式的兼容
# 修改人：张旭东 zhangxudong@genek.cn
###########################################################################

suppressPackageStartupMessages(library(optparse))
suppressPackageStartupMessages(library(CALDER))

AVAILABLE_REFERENCE_TRACKS_GENOMES <- c("hg19", "hg38", "mm9", "mm10")
INPUT_TYPES <- c("hic", "cool", "mcool")
CHROMS_TO_REMOVE <- c("ALL", "M", "chrM", "MT", "chrMT", "Y", "chrY")


parse_arguments <- function(){
	# Creating the argument parsing options
	option_list = list(
	  make_option(c("-i", "--input"), action="store", default=NA, type='character',
	              help="Input Hi-C contacts"),
	  # 增加对 mcool 格式的兼容
	  make_option(c("-t", "--type"), action="store", default='hic', type='character',
	              help="The type of input: hic or cool or mcool [default %default]"),
	  make_option(c("-b", "--bin_size"), action="store", default=50000, type='integer',
	              help="Bin size to use for the analysis [default %default]"),
	  make_option(c("-g", "--genome"), action="store", default="hg19", type='character',
	              help="Genome assembly to use [default %default]"),
	  make_option(c("-f", "--feature_track"), action="store", default=NA, type='character',
	              help="Genomic feature track to be used to determine A/B compartment direction
	              when genome == 'others'. The track should presumably have higher values
	              in A than in B compartmnets. [default %default]"),
	  # 增加了原染色体前缀参数
	  make_option(c("--chr_prefix"), action="store", default="chr", type='character',
	              help="old chr prefix [default %default]"),
	  make_option(c("-c", "--chromosomes"), action='store', default='all', type='character',
	  			  help="Chromosomes to analyze, separated by comma. [default %default]"),
	  make_option(c("-p", "--nproc"), action="store", default=1, type='integer',
	              help="Number of cores to use [default %default]"),
	  make_option(c("-o", "--outpath"), action="store", default=NA, type='character',
	              help="Path to the output folder"),
	  make_option(c("-k", "--keep_intermediate"), action="store_true", default=FALSE, type='logical',
	              help="Keep intermediate data after done [default %default]"),
	  make_option(c("-a", "--adaptive"), action="store_true", default=FALSE, type='logical',
	              help="Use adaptive resolution choice [default %default]")
	)
	parser <- OptionParser(usage = "%prog [options]", option_list=option_list)
	opt <- parse_args(parser)

	# Checking if input path exists
	if(is.na(opt$input)){
		print_help(parser)
		stop(paste0("Input path (", opt$input,") does not exist"))
	}

	# Checking if output path is provided
	if(is.na(opt$outpath)){
		stop("Output path was not provided")
	}

	# Check that the input type is one of the possible ones
	if(!(opt$type %in% INPUT_TYPES)){
		stop(paste0("Input type ", opt$input_type, " not available"))
	}

	# Check if the provided genome is in the list of available reference genomes 
	# or if a feature track is provided
	if((!(opt$genome %in% AVAILABLE_REFERENCE_TRACKS_GENOMES)) || (file.exists(opt$feature_track))){
		# in this case, we just assign it the name 'others'
		opt$genome = "others"
	}

	writeLines(c(
		"*******************************",
		"*            CALDER           *",
		"*******************************",
		paste0("[Parameters] Input: ", opt$input),
		paste0("[Parameters] Input type: ", opt$type),
		paste0("[Parameters] Bin size: ", opt$bin_size),
		paste0("[Parameters] Genome: ", opt$genome),
		paste0("[Parameters] Feature Track: ", opt$feature_track),
		paste0("[Parameters] Chr Prefix: ", opt$chr_prefix),
		paste0("[Parameters] Chromosomes: ", opt$chromosomes),
		paste0("[Parameters] N. cores: ", opt$nproc),
		paste0("[Parameters] Output: ", opt$outpath),
		paste0("[Parameters] Keep Intermediate data: ", opt$keep_intermediate),
		paste0("[Parameters] Use adaptive resolution: ", opt$adaptive)
	))

	if(file.exists(opt$feature_track)){
		opt$feature_track <- read.table(opt$feature_track, header = F)
	}

	return(opt)
}

sanitize_chroms <- function(chroms){
	res <- lapply(chroms, function(x){
		if(startsWith(x, opt$chr_prefix)){
			return(substring(x, 4))
		} else{
			return(x)
		}
	})
	return(res)
}

handle_input_hic <- function(opt){
	suppressPackageStartupMessages(library(strawr))
	chromsizes <- readHicChroms(opt$input)
	if(opt$chromosomes == "all"){
		chroms <- chromsizes[!(toupper(chromsizes$name) %in% toupper(CHROMS_TO_REMOVE)), "name"]
	}
	else{
		chrom_list <- strsplit(opt$chromosomes, ",")[[1]]
		chroms <- chromsizes[chromsizes$name %in% chrom_list, "name"]
	}
	chroms <- sanitize_chroms(chroms)
	CALDER(contact_file_hic = opt$input,
		   chrs = chroms,
		   bin_size = opt$bin_size,
		   genome = opt$genome,
		   save_dir=opt$outpath,
		   save_intermediate_data=TRUE,
		   feature_track=opt$feature_track,
		   single_binsize_only=!opt$adaptive,
		   n_cores = opt$nproc,
		   sub_domains=F)
}

# 增加了对 mcool 的支持
handle_input_mcool <- function(opt){
	intermediate_data_dir = file.path(opt$outpath, "intermediate_data")
	dir.create(intermediate_data_dir, recursive=TRUE, showWarnings=FALSE)

	opt$feature_track[, 1] = gsub(paste0("^", opt$chr_prefix), "chr", opt$feature_track[, 1])

	system(paste0("cooler dump --table chroms --out ", 
				  file.path(intermediate_data_dir, "chroms.txt"), 
				  " --header ", 
				  opt$input,
				  "::/resolutions/",
				  opt$bin_size
				  ))
	chroms <- read.table(file.path(intermediate_data_dir, "chroms.txt"), sep="\t", header=TRUE)
	if(opt$chromosomes == "all"){
		chroms <- chroms[!( toupper(chroms$name) %in% toupper(CHROMS_TO_REMOVE) ), "name"]
	}
	else{
		chrom_list <- strsplit(opt$chromosomes, ",")[[1]]
		chroms <- chroms[chroms$name %in% chrom_list, "name"]
	}
	
	dump_paths <- list()
	for(chrom in chroms){
		cat(paste0("[Pre-processing] Dumping ", chrom, "\n"))
		chrom_dump_path <- file.path(intermediate_data_dir, paste0(chrom, "_dump.txt"))
		dump_paths <- c(dump_paths, chrom_dump_path)
		if(! file.exists(chrom_dump_path)){
			system(paste0("cooler dump --table pixels --range ", 
						  chrom, 
						  " --join --balanced ",
						  opt$input,
						  "::/resolutions/",
						  opt$bin_size,						  
						  " | cut -f2,5,8 | awk '{if ($3) print;}' > ",
						  chrom_dump_path))
		}
	}

	chroms <- sanitize_chroms(chroms)
	names(dump_paths) <- chroms

	CALDER(contact_file_dump=dump_paths, 
		   chrs=chroms, 
		   bin_size=opt$bin_size,
		   genome=opt$genome,
		   save_dir=opt$outpath,
		   feature_track=opt$feature_track,
		   single_binsize_only=!opt$adaptive,
		   save_intermediate_data=TRUE,
		   n_cores=opt$nproc,
		   sub_domains=F)

}

handle_input_cool <- function(opt){
  intermediate_data_dir = file.path(opt$outpath, "intermediate_data")
  dir.create(intermediate_data_dir, recursive=TRUE, showWarnings=FALSE)
  # 处理染色体前缀
  opt$feature_track[, 1] = gsub(paste0("^", opt$chr_prefix), "chr", opt$feature_track[, 1])
  
  system(paste0("cooler dump --table chroms --out ", 
                file.path(intermediate_data_dir, "chroms.txt"), 
                " --header ", 
                opt$input
  ))
  chroms <- read.table(file.path(intermediate_data_dir, "chroms.txt"), sep="\t", header=TRUE)
  if(opt$chromosomes == "all"){
    chroms <- chroms[!( toupper(chroms$name) %in% toupper(CHROMS_TO_REMOVE) ), "name"]
  }
  else{
    chrom_list <- strsplit(opt$chromosomes, ",")[[1]]
    chroms <- chroms[chroms$name %in% chrom_list, "name"]
  }
  
  dump_paths <- list()
  for(chrom in chroms){
    cat(paste0("[Pre-processing] Dumping ", chrom, "\n"))
    chrom_dump_path <- file.path(intermediate_data_dir, paste0(chrom, "_dump.txt"))
    dump_paths <- c(dump_paths, chrom_dump_path)
    if(! file.exists(chrom_dump_path)){
      system(paste0("cooler dump --table pixels --range ", 
                    chrom, 
                    " --join --balanced ",
                    opt$input,
                    " | cut -f2,5,8 | awk '{if ($3) print;}' > ",
                    chrom_dump_path))
    }
  }
  
  chroms <- sanitize_chroms(chroms)
  names(dump_paths) <- chroms
  
  CALDER(contact_file_dump=dump_paths, 
         chrs=chroms, 
         bin_size=opt$bin_size,
         genome=opt$genome,
         save_dir=opt$outpath,
         feature_track=opt$feature_track,
         single_binsize_only=!opt$adaptive,
         save_intermediate_data=TRUE,
         n_cores=opt$nproc,
         sub_domains=F)
  
}

opt <- parse_arguments()

if(opt$type == "hic"){
	handle_input_hic(opt)
} else if(opt$type == "mcool"){
	handle_input_mcool(opt)
} else if(opt$type == "cool"){
  handle_input_cool(opt)
} else {
	stop("Unknown input type")
}

# Cleaning the output
intermediate_data_dir = file.path(opt$outpath, "intermediate_data")
if(dir.exists(intermediate_data_dir) && (!opt$keep_intermediate)){
	cat('[Post-processing] Removing intermediate data\n')
	unlink(intermediate_data_dir, recursive=TRUE)
}
exec_time_file = "./total_execution.time"
if(file.exists(exec_time_file)){
	cat("[Post-processing] Removing total_execution.time\n")
	file.remove(exec_time_file)
}

# 将 chr 再重新替换为原来的前缀
replace_chr_in_files <- function(dir_path, old_prefix, new_prefix) {
  # 定义常见的文本文件扩展名
  text_file_extensions <- c("txt", "tsv", "csv", "bed")
  
  # 获取目录中的所有文件和子目录
  files <- list.files(dir_path, recursive = TRUE, full.names = TRUE)
  
  for (file in files) {
    # 获取文件扩展名
    file_ext <- tools::file_ext(file)
    
    # 检查文件是否为文本文件
    if (file.info(file)$isdir == FALSE && file_ext %in% text_file_extensions) {
      tryCatch({
        # 读取文件内容
        content <- readLines(file)
        
        # 替换行首的 'chr' 为 'Chr'
        content <- gsub(paste0("^", old_prefix), new_prefix, content)
        
        # 写回文件
        writeLines(content, file)
        
        cat("Processed:", file, "\n")
      }, error = function(e) {
        cat("Failed to process:", file, "\n", e, "\n")
      })
    }
  }
}

# 示例用法
replace_chr_in_files(opt$outpath, "^chr", opt$chr_prefix)