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comparison ideas_preprocessor.R @ 3:e97851e8951b draft

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author greg
date Tue, 23 Jan 2018 10:48:38 -0500
parents 91c5dbb14a13
children 2b4e1bd725f7
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2:248b5f72fc02 3:e97851e8951b
2 2
3 suppressPackageStartupMessages(library("data.table")) 3 suppressPackageStartupMessages(library("data.table"))
4 suppressPackageStartupMessages(library("optparse")) 4 suppressPackageStartupMessages(library("optparse"))
5 5
6 option_list <- list( 6 option_list <- list(
7 make_option(c("--bed_input"), action="store", dest="bed_input", defaul=NULL, help="Chromosome windows positions file"), 7 make_option(c("--bed_input"), action="store", dest="bed_input", defaul=NULL, help="Chromosome windows positions file"),
8 make_option(c("--exclude_input"), action="store", dest="exclude_input", defaul=NULL, help="File(s) containing regions to exclude"), 8 make_option(c("--exclude_input"), action="store", dest="exclude_input", defaul=NULL, help="File(s) containing regions to exclude"),
9 make_option(c("--bychr"), action="store_true", dest="bychr", defaul=FALSE, help="Separate files by chromosome"), 9 make_option(c("--bychr"), action="store_true", dest="bychr", defaul=FALSE, help="Separate files by chromosome"),
10 make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", default=NULL, help="Chromosome lengths file"), 10 make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", default=NULL, help="Chromosome lengths file"),
11 make_option(c("--output"), action="store", dest="output", help="Primary output dataset"), 11 make_option(c("--output"), action="store", dest="output", help="Primary output dataset"),
12 make_option(c("--output_files_path"), action="store", dest="output_files_path", help="Primary output dataset extra files path"), 12 make_option(c("--output_files_path"), action="store", dest="output_files_path", help="Primary output dataset extra files path"),
13 make_option(c("--prep_input_config"), action="store", dest="prep_input_config", help="Preprocessing input config file"), 13 make_option(c("--prep_input_config"), action="store", dest="prep_input_config", help="Preprocessing input config file"),
14 make_option(c("--reads_per_bp"), action="store", dest="reads_per_bp", type="integer", help="Calculate the signal in each genomic window"), 14 make_option(c("--prep_output_config"), action="store", dest="prep_output_config", help="Preprocessing output config file"),
15 make_option(c("--restrict_to_chroms"), action="store", dest="restrict_to_chroms", default=NULL, help="Restrict processing to specified chromosomes"), 15 make_option(c("--reads_per_bp"), action="store", dest="reads_per_bp", type="integer", help="Calculate the signal in each genomic window"),
16 make_option(c("--standardize_datasets"), action="store_true", dest="standardize_datasets", default=FALSE, help="Standardize all datasets"), 16 make_option(c("--restrict_to_chroms"), action="store", dest="restrict_to_chroms", default=NULL, help="Restrict processing to specified chromosomes"),
17 make_option(c("--window_size"), action="store", dest="window_size", type="integer", default=NULL, help="Window size in base pairs") 17 make_option(c("--standardize_datasets"), action="store_true", dest="standardize_datasets", default=FALSE, help="Standardize all datasets"),
18 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"),
19 make_option(c("--window_size"), action="store", dest="window_size", type="integer", default=NULL, help="Window size in base pairs")
18 ) 20 )
19 21
20 parser <- OptionParser(usage="%prog [options] file", option_list=option_list) 22 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
21 args <- parse_args(parser, positional_arguments=TRUE) 23 args <- parse_args(parser, positional_arguments=TRUE)
22 opt <- args$options 24 opt <- args$options
23 25
24 create_primary_html = function(output, output_files_path) { 26 create_primary_html = function(output, output_files_path) {
25 tmp_files = list.files(path=output_files_path); 27 files = list.files(path=output_files_path, pattern="\\.txt");
26 s <- paste('<html><head></head><body>', sep="\n"); 28 s <- paste('<html><head></head><body>', sep="\n");
27 s <- paste(s, '<h3>Contents of directory required by IDEAS</h3>\n', sep=""); 29 s <- paste(s, '<h3>Contents of directory required by IDEAS</h3>\n', sep="");
28 s <- paste(s, '<ul>\n', sep=""); 30 s <- paste(s, '<ul>\n', sep="");
29 s <- paste(s, '<li><a href="prep_output_config.txt">', prep_output_config.txt, '</a></li>\n', sep=""); 31 for (i in 1:length(files)) {
30 for (i in 1:length(tmp_files)) { 32 s <- paste(s, '<li><a href="', files[i], '">', files[i], '</a></li>\n', sep="");
31 s <- paste(s, '<li><a href="', 'tmp/', tmp_files[i], '">', tmp_files[i], '</a></li>\n', sep="");
32 } 33 }
34 s <- paste(s, '<li><a href="tmp">tmp</a></li>\n', sep="");
33 s <- paste(s, '</ul>\n</body>\n</html>', sep=""); 35 s <- paste(s, '</ul>\n</body>\n</html>', sep="");
34 cat(s, file=output); 36 cat(s, file=output);
35 } 37 }
36 38
37 # Create the directories that will contain all of the output files. 39 tmp_dir = "tmp";
38 dir.create(opt$output_files_path, showWarnings=FALSE); 40 output_tmp_dir = paste(opt$output_files_path, tmp_dir, sep="/");
39 dir.create(paste(opt$output_files_path, "tmp", sep="/"), showWarnings=FALSE); 41 dir.create(output_tmp_dir, showWarnings=FALSE);
40 42
41 # Read the prep_input_config text file which has this format: 43 # Read the prep_input_config text file which has this format:
42 # "cell type name" "epigenetic factor name" "file path" "file name" "datatype" 44 # "cell type name" "epigenetic factor name" "file path" "file name" "datatype"
43 prep_input_config_matrix = as.matrix(read.table(opt$prep_input_config)); 45 prep_input_config_matrix = as.matrix(read.table(opt$prep_input_config));
44 # Process data to windows mean. 46 # Process data to windows mean.
45 for (i in 1:dim(prep_input_config_matrix)[1]) { 47 for (i in 1:dim(prep_input_config_matrix)[1]) {
46 file_path = prep_input_config_matrix[i, 3] 48 file_path = prep_input_config_matrix[i, 3]
47 file_name = prep_input_config_matrix[i, 4] 49 file_name = prep_input_config_matrix[i, 4]
48 datatype = prep_input_config_matrix[i, 5] 50 datatype = prep_input_config_matrix[i, 5]
49 if (datatype == "bam") { 51 if (datatype == "bam") {
50 system(paste("samtools index", file_path)); 52 cmd = paste("samtools index", file_path);
51 bw = paste(file_name, "bw", sep="."); 53 system(cmd);
52 system(paste("bamCoverage --bam", file_path, "-o", bw, "--binSize", opt$window_size)); 54 bigwig_file_name = paste(file_name, "bw", sep=".");
55 cmd = paste("bamCoverage --bam", file_path, "-o", bigwig_file_name, "--binSize", opt$window_size);
56 system(cmd);
53 } else { 57 } else {
54 bw = file_path; 58 bigwig_file_name = file_path;
55 } 59 }
56 bd = paste(output_files_path, "tmp", file_name, ".bed", sep="/"); 60 bed_file_name = paste(file_name, "bed", sep=".");
57 system(paste("bigWigAverageOverBed", bw, opt$bed_input, "stdout | cut -f5 >", bd)); 61 bed_file_path = paste("tmp", bed_file_name, sep="/");
58 system(paste("gzip -f", bd)); 62 cmd = paste("bigWigAverageOverBed", bigwig_file_name, opt$bed_input, "stdout | cut -f5 >", bed_file_path);
63 system(cmd);
64 cmd = paste("gzip -f", bed_file_path);
65 system(cmd);
59 } 66 }
60 67
68 # Create file1.txt.
69 cmd = paste("cut -d' '", opt$prep_input_config, "-f1,2 > file1.txt", sep=" ");
70 system(cmd);
71 # Compress the bed files in the tmp directory.
72 tmp_gzipped_files = paste(tmp_dir, "*.bed.gz", sep="/");
73 # Create file2.txt.
74 cmd = paste("ls", tmp_gzipped_files, "> file2.txt", sep=" ");
75 system(cmd);
76 # Create the prep_output_config with the format required by IDEAS.
77 cmd = paste("paste -d' ' file1.txt file2.txt >", opt$prep_output_config, sep=" ");
78 system(cmd);
79 # Move the prep_output_config to the output directory.
80 to_path = paste(opt$output_files_path, opt$prep_output_config, sep="/");
81 file.rename(opt$prep_output_config, to_path);
82 # Move the compressed bed files in the tmp
83 # directory to the output tmp directory.
84 tmp_files = list.files(path=tmp_dir);
85 for (i in 1:length(tmp_files)) {
86 from_path = paste(tmp_dir, tmp_files[i], sep="/");
87 to_path = paste(output_tmp_dir, tmp_files[i], sep="/");
88 file.rename(from_path, to_path);
89 }
90 if (!is.null(opt$windows_positions_by_chroms_config)) {
91 # Move the windows_positions_by_chroms_config to the output directory.
92 to_path = paste(opt$output_files_path, opt$windows_positions_by_chroms_config, sep="/");
93 file.rename(opt$windows_positions_by_chroms_config, to_path);
94 }
61 # Create the primary HTML dataset. 95 # Create the primary HTML dataset.
62 create_primary_html(opt$output, opt$output_files_path); 96 create_primary_html(opt$output, opt$output_files_path);