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comparison ideas_preprocessor.R @ 25:f7563bb242fc draft

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author greg
date Thu, 01 Feb 2018 11:22:27 -0500
parents 3651f1592f3f
children 19881f817d25
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24:71345e154c66 25:f7563bb242fc
30 ) 30 )
31 31
32 parser <- OptionParser(usage="%prog [options] file", option_list=option_list) 32 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
33 args <- parse_args(parser, positional_arguments=TRUE) 33 args <- parse_args(parser, positional_arguments=TRUE)
34 opt <- args$options 34 opt <- args$options
35
36 create_primary_html = function(output, output_files_path) {
37 files = list.files(path=output_files_path);
38 s <- paste('<html><head></head><body>', sep="\n");
39 s <- paste(s, '<h3>Files prepared for IDEAS</h3>\n', sep="");
40 s <- paste(s, '<ul>\n', sep="");
41 for (i in 1:length(files)) {
42 s <- paste(s, '<li><a href="', files[i], '">', files[i], '</a></li>\n', sep="");
43 }
44 s <- paste(s, '</ul></body></html>', sep="");
45 cat(s, file=output);
46 }
47 35
48 tmp_dir = "tmp"; 36 tmp_dir = "tmp";
49 37
50 # Read the ideaspre_input_config text file which has this format: 38 # Read the ideaspre_input_config text file which has this format:
51 # "cell type name" "epigenetic factor name" "file path" "file name" "datatype" 39 # "cell type name" "epigenetic factor name" "file path" "file name" "datatype"
97 to_path = paste(opt$output_files_path, ideas_input_config, sep="/"); 85 to_path = paste(opt$output_files_path, ideas_input_config, sep="/");
98 file.rename(ideas_input_config, to_path); 86 file.rename(ideas_input_config, to_path);
99 # Archive the tmp directory. 87 # Archive the tmp directory.
100 cmd = "tar -cvf tmp.tar tmp"; 88 cmd = "tar -cvf tmp.tar tmp";
101 system(cmd); 89 system(cmd);
90 # Compress the archive.
91 cmd = "gzip tmp.tar";
92 system(cmd);
102 # Move the tmp archive to the output directory. 93 # Move the tmp archive to the output directory.
103 to_path = paste(opt$output_files_path, "tmp.tar", sep="/"); 94 to_path = paste(opt$output_files_path, "tmp.tar.gz", sep="/");
104 file.rename("tmp.tar", to_path); 95 file.rename("tmp.tar.gz", to_path);
105 96
106 if (!is.null(opt$chrom_bed_input) && !is.null(opt$chromosome_windows)) { 97 if (!is.null(opt$chrom_bed_input) && !is.null(opt$chromosome_windows)) {
107 # Renane opt$chrom_bed_input to be chromosomes.bed 98 # Renane opt$chrom_bed_input to be chromosomes.bed
108 # and make a copy of it in the output directory. 99 # and make a copy of it in the output directory.
109 to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/"); 100 to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/");
110 file.copy(opt$chrom_bed_input, to_path); 101 file.copy(opt$chrom_bed_input, to_path);
111 # Move chromosome_windows.txt to the output directory. 102 # Move chromosome_windows.txt to the output directory.
112 to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/"); 103 to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/");
113 file.rename(opt$chromosome_windows, to_path); 104 file.rename(opt$chromosome_windows, to_path);
114 } 105 }
115 # Create the primary HTML dataset. 106
116 create_primary_html(opt$output, opt$output_files_path);