Mercurial > repos > greg > ideas_preprocessor

changeset 5:2b4e1bd725f7 draft

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Uploaded
author greg
date Wed, 24 Jan 2018 08:30:05 -0500
parents f577a83e86c4
children 6fe65d1379a8
files ideas_preprocessor.R
diffstat 1 files changed, 34 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- 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('<html><head></head><body>', sep="\n");
-    s <- paste(s, '<h3>Contents of directory required by IDEAS</h3>\n', sep="");
+    s <- paste(s, '<h3>History item ', output_hid, ' files prepared for IDEAS</h3>\n', sep="");
     s <- paste(s, '<ul>\n', sep="");
     for (i in 1:length(files)) {
         s <- paste(s, '<li><a href="', files[i], '">', files[i], '</a></li>\n', sep="");
     }
-    s <- paste(s, '<li><a href="tmp">tmp</a></li>\n', sep="");
     s <- paste(s, '</ul>\n</body>\n</html>', 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);