# HG changeset patch # User greg # Date 1516649728 18000 # Node ID 91c5dbb14a13d0bb0fdf3350e23b743044f560eb # Parent f060a0fbd4fe528381f0e8e0f2fd8d2d83b19b15 Uploaded diff -r f060a0fbd4fe -r 91c5dbb14a13 ideas_preprocessor.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ideas_preprocessor.R Mon Jan 22 14:35:28 2018 -0500 @@ -0,0 +1,62 @@ +#!/usr/bin/env Rscript + +suppressPackageStartupMessages(library("data.table")) +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") +) + +parser <- OptionParser(usage="%prog [options] file", option_list=option_list) +args <- parse_args(parser, positional_arguments=TRUE) +opt <- args$options + +create_primary_html = function(output, output_files_path) { + tmp_files = list.files(path=output_files_path); + 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); + +# Read the prep_input_config text file which has this format: +# "cell type name" "epigenetic factor name" "file path" "file name" "datatype" +prep_input_config_matrix = as.matrix(read.table(opt$prep_input_config)); +# Process data to windows mean. +for (i in 1:dim(prep_input_config_matrix)[1]) { + file_path = prep_input_config_matrix[i, 3] + file_name = prep_input_config_matrix[i, 4] + datatype = prep_input_config_matrix[i, 5] + if (datatype == "bam") { + system(paste("samtools index", file_path)); + bw = paste(file_name, "bw", sep="."); + system(paste("bamCoverage --bam", file_path, "-o", bw, "--binSize", opt$window_size)); + } else { + bw = file_path; + } + bd = paste(output_files_path, "tmp", file_name, ".bed", sep="/"); + system(paste("bigWigAverageOverBed", bw, opt$bed_input, "stdout | cut -f5 >", bd)); + system(paste("gzip -f", bd)); +} + +# Create the primary HTML dataset. +create_primary_html(opt$output, opt$output_files_path);