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comparison ideas_preprocessor.R @ 5:2b4e1bd725f7 draft

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author greg
date Wed, 24 Jan 2018 08:30:05 -0500
parents e97851e8951b
children 92bb33490bb4
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4:f577a83e86c4 5:2b4e1bd725f7
1 (.venv) [galaxy@IDEAS ideas_preprocessor]$ cat ideas_preprocessor.R
1 #!/usr/bin/env Rscript 2 #!/usr/bin/env Rscript
2 3
3 suppressPackageStartupMessages(library("data.table")) 4 suppressPackageStartupMessages(library("data.table"))
4 suppressPackageStartupMessages(library("optparse")) 5 suppressPackageStartupMessages(library("optparse"))
5 6
6 option_list <- list( 7 option_list <- list(
7 make_option(c("--bed_input"), action="store", dest="bed_input", defaul=NULL, help="Chromosome windows positions file"), 8 make_option(c("--chrom_bed_input"), action="store", dest="chrom_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"), 9 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"), 10 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"), 11 make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", default=NULL, help="Chromosome lengths file"),
12 make_option(c("--ideas_input_config"), action="store", dest="ideas_input_config", help="Preprocessing output config file"),
13 make_option(c("--ideaspre_input_config"), action="store", dest="ideaspre_input_config", help="Preprocessing input config file"),
11 make_option(c("--output"), action="store", dest="output", help="Primary output dataset"), 14 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"), 15 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"), 16 make_option(c("--output_hid"), action="store", dest="output_hid", help="Primary output dataset hid"),
14 make_option(c("--prep_output_config"), action="store", dest="prep_output_config", help="Preprocessing output config file"),
15 make_option(c("--reads_per_bp"), action="store", dest="reads_per_bp", type="integer", help="Calculate the signal in each genomic window"), 17 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("--restrict_to_chroms"), action="store", dest="restrict_to_chroms", default=NULL, help="Restrict processing to specified chromosomes"), 18 make_option(c("--restrict_to_chroms"), action="store", dest="restrict_to_chroms", default=NULL, help="Restrict processing to specified chromosomes"),
17 make_option(c("--standardize_datasets"), action="store_true", dest="standardize_datasets", default=FALSE, help="Standardize all datasets"), 19 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"), 20 make_option(c("--chromosome_windows"), action="store", dest="chromosome_windows", 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") 21 make_option(c("--window_size"), action="store", dest="window_size", type="integer", default=NULL, help="Window size in base pairs")
20 ) 22 )
21 23
22 parser <- OptionParser(usage="%prog [options] file", option_list=option_list) 24 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
23 args <- parse_args(parser, positional_arguments=TRUE) 25 args <- parse_args(parser, positional_arguments=TRUE)
24 opt <- args$options 26 opt <- args$options
25 27
26 create_primary_html = function(output, output_files_path) { 28 create_primary_html = function(output, output_hid, output_files_path) {
27 files = list.files(path=output_files_path, pattern="\\.txt"); 29 files = list.files(path=output_files_path);
28 s <- paste('<html><head></head><body>', sep="\n"); 30 s <- paste('<html><head></head><body>', sep="\n");
29 s <- paste(s, '<h3>Contents of directory required by IDEAS</h3>\n', sep=""); 31 s <- paste(s, '<h3>History item ', output_hid, ' files prepared for IDEAS</h3>\n', sep="");
30 s <- paste(s, '<ul>\n', sep=""); 32 s <- paste(s, '<ul>\n', sep="");
31 for (i in 1:length(files)) { 33 for (i in 1:length(files)) {
32 s <- paste(s, '<li><a href="', files[i], '">', files[i], '</a></li>\n', sep=""); 34 s <- paste(s, '<li><a href="', files[i], '">', files[i], '</a></li>\n', sep="");
33 } 35 }
34 s <- paste(s, '<li><a href="tmp">tmp</a></li>\n', sep="");
35 s <- paste(s, '</ul>\n</body>\n</html>', sep=""); 36 s <- paste(s, '</ul>\n</body>\n</html>', sep="");
36 cat(s, file=output); 37 cat(s, file=output);
37 } 38 }
38 39
39 tmp_dir = "tmp"; 40 tmp_dir = "tmp";
40 output_tmp_dir = paste(opt$output_files_path, tmp_dir, sep="/"); 41 output_tmp_dir = paste(opt$output_files_path, tmp_dir, sep="/");
41 dir.create(output_tmp_dir, showWarnings=FALSE); 42 dir.create(output_tmp_dir, showWarnings=FALSE);
42 43
43 # Read the prep_input_config text file which has this format: 44 # Read the ideaspre_input_config text file which has this format:
44 # "cell type name" "epigenetic factor name" "file path" "file name" "datatype" 45 # "cell type name" "epigenetic factor name" "file path" "file name" "datatype"
45 prep_input_config_matrix = as.matrix(read.table(opt$prep_input_config)); 46 ideaspre_input_config = as.matrix(read.table(opt$ideaspre_input_config));
46 # Process data to windows mean. 47 # Process data to windows mean.
47 for (i in 1:dim(prep_input_config_matrix)[1]) { 48 for (i in 1:dim(ideaspre_input_config)[1]) {
48 file_path = prep_input_config_matrix[i, 3] 49 file_path = ideaspre_input_config[i, 3]
49 file_name = prep_input_config_matrix[i, 4] 50 file_name = ideaspre_input_config[i, 4]
50 datatype = prep_input_config_matrix[i, 5] 51 datatype = ideaspre_input_config[i, 5]
51 if (datatype == "bam") { 52 if (datatype == "bam") {
52 cmd = paste("samtools index", file_path); 53 cmd = paste("samtools index", file_path);
53 system(cmd); 54 system(cmd);
54 bigwig_file_name = paste(file_name, "bw", sep="."); 55 bigwig_file_name = paste(file_name, "bw", sep=".");
55 cmd = paste("bamCoverage --bam", file_path, "-o", bigwig_file_name, "--binSize", opt$window_size); 56 cmd = paste("bamCoverage --bam", file_path, "-o", bigwig_file_name, "--binSize", opt$window_size);
57 } else { 58 } else {
58 bigwig_file_name = file_path; 59 bigwig_file_name = file_path;
59 } 60 }
60 bed_file_name = paste(file_name, "bed", sep="."); 61 bed_file_name = paste(file_name, "bed", sep=".");
61 bed_file_path = paste("tmp", bed_file_name, sep="/"); 62 bed_file_path = paste("tmp", bed_file_name, sep="/");
62 cmd = paste("bigWigAverageOverBed", bigwig_file_name, opt$bed_input, "stdout | cut -f5 >", bed_file_path); 63 cmd = paste("bigWigAverageOverBed", bigwig_file_name, opt$chrom_bed_input, "stdout | cut -f5 >", bed_file_path);
63 system(cmd); 64 system(cmd);
64 cmd = paste("gzip -f", bed_file_path); 65 cmd = paste("gzip -f", bed_file_path);
65 system(cmd); 66 system(cmd);
66 } 67 }
67 68
68 # Create file1.txt. 69 # Create temporary file1.txt.
69 cmd = paste("cut -d' '", opt$prep_input_config, "-f1,2 > file1.txt", sep=" "); 70 cmd = paste("cut -d' '", opt$ideaspre_input_config, "-f1,2 > file1.txt", sep=" ");
70 system(cmd); 71 system(cmd);
71 # Compress the bed files in the tmp directory. 72 # Compress the bed files in the tmp directory.
72 tmp_gzipped_files = paste(tmp_dir, "*.bed.gz", sep="/"); 73 tmp_gzipped_files = paste(tmp_dir, "*.bed.gz", sep="/");
73 # Create file2.txt. 74 # Create temporary file2.txt.
74 cmd = paste("ls", tmp_gzipped_files, "> file2.txt", sep=" "); 75 cmd = paste("ls", tmp_gzipped_files, "> file2.txt", sep=" ");
75 system(cmd); 76 system(cmd);
76 # Create the prep_output_config with the format required by IDEAS. 77 # Create IDEAS_input_config.txt with the format required by IDEAS.
77 cmd = paste("paste -d' ' file1.txt file2.txt >", opt$prep_output_config, sep=" "); 78 cmd = paste("paste -d' ' file1.txt file2.txt >", opt$ideas_input_config, sep=" ");
78 system(cmd); 79 system(cmd);
79 # Move the prep_output_config to the output directory. 80 # Move IDEAS_input_config.txt to the output directory.
80 to_path = paste(opt$output_files_path, opt$prep_output_config, sep="/"); 81 to_path = paste(opt$output_files_path, opt$ideas_input_config, sep="/");
81 file.rename(opt$prep_output_config, to_path); 82 file.rename(opt$ideas_input_config, to_path);
82 # Move the compressed bed files in the tmp 83 # Move all compressed bed files in the tmp
83 # directory to the output tmp directory. 84 # directory to the output tmp directory.
84 tmp_files = list.files(path=tmp_dir); 85 tmp_files = list.files(path=tmp_dir);
85 for (i in 1:length(tmp_files)) { 86 for (i in 1:length(tmp_files)) {
86 from_path = paste(tmp_dir, tmp_files[i], sep="/"); 87 from_path = paste(tmp_dir, tmp_files[i], sep="/");
87 to_path = paste(output_tmp_dir, tmp_files[i], sep="/"); 88 to_path = paste(output_tmp_dir, tmp_files[i], sep="/");
88 file.rename(from_path, to_path); 89 file.rename(from_path, to_path);
89 } 90 }
90 if (!is.null(opt$windows_positions_by_chroms_config)) { 91 if (!is.nulll(opt$chrom_bed_input) && !is.null(opt$chromosome_windows)) {
91 # Move the windows_positions_by_chroms_config to the output directory. 92 # Rename chrom_bed_input to chromosomes.txt
92 to_path = paste(opt$output_files_path, opt$windows_positions_by_chroms_config, sep="/"); 93 # and move it to the output directory.
93 file.rename(opt$windows_positions_by_chroms_config, to_path); 94 to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/");
95 file.rename(opt$chrom_bed_input, to_path)
96 # Move chromosome_windows.txt to the output directory.
97 to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/");
98 file.rename(opt$chromosome_windows, to_path);
94 } 99 }
95 # Create the primary HTML dataset. 100 # Create the primary HTML dataset.
96 create_primary_html(opt$output, opt$output_files_path); 101 create_primary_html(opt$output, opt$output_hid, opt$output_files_path);