# HG changeset patch # User greg # Date 1516800605 18000 # Node ID 2b4e1bd725f719aeb48b679abff455c1e34e6ece # Parent f577a83e86c4e542aa60a78aeddba398de97729e Uploaded diff -r f577a83e86c4 -r 2b4e1bd725f7 ideas_preprocessor.R --- a/ideas_preprocessor.R Wed Jan 24 08:29:58 2018 -0500 +++ b/ideas_preprocessor.R Wed Jan 24 08:30:05 2018 -0500 @@ -1,21 +1,23 @@ +(.venv) [galaxy@IDEAS ideas_preprocessor]$ cat ideas_preprocessor.R #!/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("--chrom_bed_input"), action="store", dest="chrom_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("--ideas_input_config"), action="store", dest="ideas_input_config", help="Preprocessing output config file"), + make_option(c("--ideaspre_input_config"), action="store", dest="ideaspre_input_config", help="Preprocessing input config 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("--output_hid"), action="store", dest="output_hid", help="Primary output dataset hid"), 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("--chromosome_windows"), action="store", dest="chromosome_windows", 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") ) @@ -23,15 +25,14 @@ args <- parse_args(parser, positional_arguments=TRUE) opt <- args$options -create_primary_html = function(output, output_files_path) { - files = list.files(path=output_files_path, pattern="\\.txt"); +create_primary_html = function(output, output_hid, output_files_path) { + 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, '

History item ', output_hid, ' files prepared for IDEAS

\n', sep=""); s <- paste(s, '\n\n', sep=""); cat(s, file=output); } @@ -40,14 +41,14 @@ output_tmp_dir = paste(opt$output_files_path, tmp_dir, sep="/"); dir.create(output_tmp_dir, showWarnings=FALSE); -# Read the prep_input_config text file which has this format: +# Read the ideaspre_input_config text file which has this format: # "cell type name" "epigenetic factor name" "file path" "file name" "datatype" -prep_input_config_matrix = as.matrix(read.table(opt$prep_input_config)); +ideaspre_input_config = as.matrix(read.table(opt$ideaspre_input_config)); # Process data to windows mean. -for (i in 1:dim(prep_input_config_matrix)[1]) { - file_path = prep_input_config_matrix[i, 3] - file_name = prep_input_config_matrix[i, 4] - datatype = prep_input_config_matrix[i, 5] +for (i in 1:dim(ideaspre_input_config)[1]) { + file_path = ideaspre_input_config[i, 3] + file_name = ideaspre_input_config[i, 4] + datatype = ideaspre_input_config[i, 5] if (datatype == "bam") { cmd = paste("samtools index", file_path); system(cmd); @@ -59,27 +60,27 @@ } bed_file_name = paste(file_name, "bed", sep="."); bed_file_path = paste("tmp", bed_file_name, sep="/"); - cmd = paste("bigWigAverageOverBed", bigwig_file_name, opt$bed_input, "stdout | cut -f5 >", bed_file_path); + cmd = paste("bigWigAverageOverBed", bigwig_file_name, opt$chrom_bed_input, "stdout | cut -f5 >", bed_file_path); system(cmd); cmd = paste("gzip -f", bed_file_path); system(cmd); } -# Create file1.txt. -cmd = paste("cut -d' '", opt$prep_input_config, "-f1,2 > file1.txt", sep=" "); +# Create temporary file1.txt. +cmd = paste("cut -d' '", opt$ideaspre_input_config, "-f1,2 > file1.txt", sep=" "); system(cmd); # Compress the bed files in the tmp directory. tmp_gzipped_files = paste(tmp_dir, "*.bed.gz", sep="/"); -# Create file2.txt. +# Create temporary file2.txt. cmd = paste("ls", tmp_gzipped_files, "> file2.txt", sep=" "); system(cmd); -# Create the prep_output_config with the format required by IDEAS. -cmd = paste("paste -d' ' file1.txt file2.txt >", opt$prep_output_config, sep=" "); +# Create IDEAS_input_config.txt with the format required by IDEAS. +cmd = paste("paste -d' ' file1.txt file2.txt >", opt$ideas_input_config, sep=" "); system(cmd); -# Move the prep_output_config to the output directory. -to_path = paste(opt$output_files_path, opt$prep_output_config, sep="/"); -file.rename(opt$prep_output_config, to_path); -# Move the compressed bed files in the tmp +# Move IDEAS_input_config.txt to the output directory. +to_path = paste(opt$output_files_path, opt$ideas_input_config, sep="/"); +file.rename(opt$ideas_input_config, to_path); +# Move all compressed bed files in the tmp # directory to the output tmp directory. tmp_files = list.files(path=tmp_dir); for (i in 1:length(tmp_files)) { @@ -87,10 +88,14 @@ to_path = paste(output_tmp_dir, tmp_files[i], sep="/"); file.rename(from_path, to_path); } -if (!is.null(opt$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$windows_positions_by_chroms_config, to_path); +if (!is.nulll(opt$chrom_bed_input) && !is.null(opt$chromosome_windows)) { + # Rename chrom_bed_input to chromosomes.txt + # and move it to the output directory. + to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/"); + file.rename(opt$chrom_bed_input, to_path) + # Move chromosome_windows.txt to the output directory. + to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/"); + file.rename(opt$chromosome_windows, to_path); } # Create the primary HTML dataset. -create_primary_html(opt$output, opt$output_files_path); +create_primary_html(opt$output, opt$output_hid, opt$output_files_path);