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comparison ideas_preprocessor.R @ 18:504226a7eb75 draft

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author greg
date Tue, 30 Jan 2018 13:21:00 -0500
parents ce2021cd68d2
children 99102499271a
comparison
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17:6ff92012abb7 18:504226a7eb75
20 make_option(c("--bychr"), action="store_true", dest="bychr", defaul=FALSE, help="Separate files by chromosome"), 20 make_option(c("--bychr"), action="store_true", dest="bychr", defaul=FALSE, help="Separate files by chromosome"),
21 make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", default=NULL, help="Chromosome lengths file"), 21 make_option(c("--chrom_len_file"), action="store", dest="chrom_len_file", default=NULL, help="Chromosome lengths file"),
22 make_option(c("--ideaspre_input_config"), action="store", dest="ideaspre_input_config", help="Preprocessing input config file"), 22 make_option(c("--ideaspre_input_config"), action="store", dest="ideaspre_input_config", help="Preprocessing input config file"),
23 make_option(c("--output"), action="store", dest="output", help="Primary output dataset"), 23 make_option(c("--output"), action="store", dest="output", help="Primary output dataset"),
24 make_option(c("--output_files_path"), action="store", dest="output_files_path", help="Primary output dataset extra files path"), 24 make_option(c("--output_files_path"), action="store", dest="output_files_path", help="Primary output dataset extra files path"),
25 make_option(c("--output_hid"), action="store", dest="output_hid", help="Primary output dataset hid"),
26 make_option(c("--reads_per_bp"), action="store", dest="reads_per_bp", type="integer", help="Calculate the signal in each genomic window"), 25 make_option(c("--reads_per_bp"), action="store", dest="reads_per_bp", type="integer", help="Calculate the signal in each genomic window"),
27 make_option(c("--restrict_to_chroms"), action="store", dest="restrict_to_chroms", default=NULL, help="Restrict processing to specified chromosomes"), 26 make_option(c("--restrict_to_chroms"), action="store", dest="restrict_to_chroms", default=NULL, help="Restrict processing to specified chromosomes"),
28 make_option(c("--standardize_datasets"), action="store_true", dest="standardize_datasets", default=FALSE, help="Standardize all datasets"), 27 make_option(c("--standardize_datasets"), action="store_true", dest="standardize_datasets", default=FALSE, help="Standardize all datasets"),
29 make_option(c("--chromosome_windows"), action="store", dest="chromosome_windows", default=NULL, help="Windows positions by chroms config file"), 28 make_option(c("--chromosome_windows"), action="store", dest="chromosome_windows", default=NULL, help="Windows positions by chroms config file"),
30 make_option(c("--window_size"), action="store", dest="window_size", type="integer", default=NULL, help="Window size in base pairs") 29 make_option(c("--window_size"), action="store", dest="window_size", type="integer", default=NULL, help="Window size in base pairs")
32 31
33 parser <- OptionParser(usage="%prog [options] file", option_list=option_list) 32 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
34 args <- parse_args(parser, positional_arguments=TRUE) 33 args <- parse_args(parser, positional_arguments=TRUE)
35 opt <- args$options 34 opt <- args$options
36 35
37 create_primary_html = function(output, output_hid, output_files_path) { 36 create_primary_html = function(output, output_files_path) {
38 files = list.files(path=output_files_path); 37 files = list.files(path=output_files_path);
39 s <- paste('<html><head></head><body>', sep="\n"); 38 s <- paste('<html><head></head><body>', sep="\n");
40 s <- paste(s, '<h3>History item ', output_hid, ' files prepared for IDEAS</h3>\n', sep=""); 39 s <- paste(s, '<h3>Files prepared for IDEAS</h3>\n', sep="");
41 s <- paste(s, '<ul>\n', sep=""); 40 s <- paste(s, '<ul>\n', sep="");
42 for (i in 1:length(files)) { 41 for (i in 1:length(files)) {
43 s <- paste(s, '<li><a href="', files[i], '">', files[i], '</a></li>\n', sep=""); 42 s <- paste(s, '<li><a href="', files[i], '">', files[i], '</a></li>\n', sep="");
44 } 43 }
45 s <- paste(s, '</ul>\n</body>\n</html>', sep=""); 44 s <- paste(s, '</ul>\n</body>\n</html>', sep="");
115 # Move chromosome_windows.txt to the output directory. 114 # Move chromosome_windows.txt to the output directory.
116 to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/"); 115 to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/");
117 file.rename(opt$chromosome_windows, to_path); 116 file.rename(opt$chromosome_windows, to_path);
118 } 117 }
119 # Create the primary HTML dataset. 118 # Create the primary HTML dataset.
120 create_primary_html(opt$output, opt$output_hid, opt$output_files_path); 119 create_primary_html(opt$output, opt$output_files_path);