# HG changeset patch # User greg # Date 1516722518 18000 # Node ID e97851e8951b4e4ac9a43dfea53c31c6f17de9b7 # Parent 248b5f72fc02aa458d1a7e19cb90586eb70b6f21 Uploaded diff -r 248b5f72fc02 -r e97851e8951b ideas_preprocessor.R --- a/ideas_preprocessor.R Tue Jan 23 10:48:31 2018 -0500 +++ b/ideas_preprocessor.R Tue Jan 23 10:48:38 2018 -0500 @@ -4,17 +4,19 @@ suppressPackageStartupMessages(library("optparse")) option_list <- list( - make_option(c("--bed_input"), action="store", dest="bed_input", defaul=NULL, help="Chromosome windows positions file"), - make_option(c("--exclude_input"), action="store", dest="exclude_input", defaul=NULL, help="File(s) containing regions to exclude"), - make_option(c("--bychr"), action="store_true", dest="bychr", defaul=FALSE, help="Separate files by chromosome"), - make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", default=NULL, help="Chromosome lengths file"), - make_option(c("--output"), action="store", dest="output", help="Primary output dataset"), - make_option(c("--output_files_path"), action="store", dest="output_files_path", help="Primary output dataset extra files path"), - make_option(c("--prep_input_config"), action="store", dest="prep_input_config", help="Preprocessing input config file"), - make_option(c("--reads_per_bp"), action="store", dest="reads_per_bp", type="integer", help="Calculate the signal in each genomic window"), - make_option(c("--restrict_to_chroms"), action="store", dest="restrict_to_chroms", default=NULL, help="Restrict processing to specified chromosomes"), - make_option(c("--standardize_datasets"), action="store_true", dest="standardize_datasets", default=FALSE, help="Standardize all datasets"), - make_option(c("--window_size"), action="store", dest="window_size", type="integer", default=NULL, help="Window size in base pairs") + make_option(c("--bed_input"), action="store", dest="bed_input", defaul=NULL, help="Chromosome windows positions file"), + make_option(c("--exclude_input"), action="store", dest="exclude_input", defaul=NULL, help="File(s) containing regions to exclude"), + make_option(c("--bychr"), action="store_true", dest="bychr", defaul=FALSE, help="Separate files by chromosome"), + make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", default=NULL, help="Chromosome lengths file"), + make_option(c("--output"), action="store", dest="output", help="Primary output dataset"), + make_option(c("--output_files_path"), action="store", dest="output_files_path", help="Primary output dataset extra files path"), + make_option(c("--prep_input_config"), action="store", dest="prep_input_config", help="Preprocessing input config file"), + make_option(c("--prep_output_config"), action="store", dest="prep_output_config", help="Preprocessing output config file"), + make_option(c("--reads_per_bp"), action="store", dest="reads_per_bp", type="integer", help="Calculate the signal in each genomic window"), + make_option(c("--restrict_to_chroms"), action="store", dest="restrict_to_chroms", default=NULL, help="Restrict processing to specified chromosomes"), + make_option(c("--standardize_datasets"), action="store_true", dest="standardize_datasets", default=FALSE, help="Standardize all datasets"), + make_option(c("--windows_positions_by_chroms_config"), action="store", dest="windows_positions_by_chroms_config", default=NULL, help="Windows positions by chroms config file"), + make_option(c("--window_size"), action="store", dest="window_size", type="integer", default=NULL, help="Window size in base pairs") ) parser <- OptionParser(usage="%prog [options] file", option_list=option_list) @@ -22,21 +24,21 @@ opt <- args$options create_primary_html = function(output, output_files_path) { - tmp_files = list.files(path=output_files_path); + files = list.files(path=output_files_path, pattern="\\.txt"); s <- paste('', sep="\n"); s <- paste(s, '

Contents of directory required by IDEAS

\n', sep=""); s <- paste(s, '\n\n', sep=""); cat(s, file=output); } -# Create the directories that will contain all of the output files. -dir.create(opt$output_files_path, showWarnings=FALSE); -dir.create(paste(opt$output_files_path, "tmp", sep="/"), showWarnings=FALSE); +tmp_dir = "tmp"; +output_tmp_dir = paste(opt$output_files_path, tmp_dir, sep="/"); +dir.create(output_tmp_dir, showWarnings=FALSE); # Read the prep_input_config text file which has this format: # "cell type name" "epigenetic factor name" "file path" "file name" "datatype" @@ -47,16 +49,48 @@ file_name = prep_input_config_matrix[i, 4] datatype = prep_input_config_matrix[i, 5] if (datatype == "bam") { - system(paste("samtools index", file_path)); - bw = paste(file_name, "bw", sep="."); - system(paste("bamCoverage --bam", file_path, "-o", bw, "--binSize", opt$window_size)); + cmd = paste("samtools index", file_path); + system(cmd); + bigwig_file_name = paste(file_name, "bw", sep="."); + cmd = paste("bamCoverage --bam", file_path, "-o", bigwig_file_name, "--binSize", opt$window_size); + system(cmd); } else { - bw = file_path; + bigwig_file_name = file_path; } - bd = paste(output_files_path, "tmp", file_name, ".bed", sep="/"); - system(paste("bigWigAverageOverBed", bw, opt$bed_input, "stdout | cut -f5 >", bd)); - system(paste("gzip -f", bd)); + bed_file_name = paste(file_name, "bed", sep="."); + bed_file_path = paste("tmp", bed_file_name, sep="/"); + cmd = paste("bigWigAverageOverBed", bigwig_file_name, opt$bed_input, "stdout | cut -f5 >", bed_file_path); + system(cmd); + cmd = paste("gzip -f", bed_file_path); + system(cmd); } +# Create file1.txt. +cmd = paste("cut -d' '", opt$prep_input_config, "-f1,2 > file1.txt", sep=" "); +system(cmd); +# Compress the bed files in the tmp directory. +tmp_gzipped_files = paste(tmp_dir, "*.bed.gz", sep="/"); +# Create file2.txt. +cmd = paste("ls", tmp_gzipped_files, "> file2.txt", sep=" "); +system(cmd); +# Create the prep_output_config with the format required by IDEAS. +cmd = paste("paste -d' ' file1.txt file2.txt >", opt$prep_output_config, sep=" "); +system(cmd); +# Move the prep_output_config to the output directory. +to_path = paste(opt$output_files_path, opt$prep_output_config, sep="/"); +file.rename(opt$prep_output_config, to_path); +# Move the compressed bed files in the tmp +# directory to the output tmp directory. +tmp_files = list.files(path=tmp_dir); +for (i in 1:length(tmp_files)) { + from_path = paste(tmp_dir, tmp_files[i], sep="/"); + to_path = paste(output_tmp_dir, tmp_files[i], sep="/"); + file.rename(from_path, to_path); +} +if (!is.null(opt$windows_positions_by_chroms_config)) { + # Move the windows_positions_by_chroms_config to the output directory. + to_path = paste(opt$output_files_path, opt$windows_positions_by_chroms_config, sep="/"); + file.rename(opt$windows_positions_by_chroms_config, to_path); +} # Create the primary HTML dataset. create_primary_html(opt$output, opt$output_files_path);