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comparison create_heatmaps.R @ 163:9ab14f7f66c8 draft

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author greg
date Fri, 12 Jan 2018 14:51:42 -0500
parents 19142fc18b2d
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162:19142fc18b2d 163:9ab14f7f66c8
11 11
12 parser <- OptionParser(usage="%prog [options] file", option_list=option_list); 12 parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
13 args <- parse_args(parser, positional_arguments=TRUE); 13 args <- parse_args(parser, positional_arguments=TRUE);
14 opt <- args$options; 14 opt <- args$options;
15 15
16 heatmap_path <- paste(opt$script_dir, "create_heatmap.R", sep="/"); 16 heatmap_path = paste(opt$script_dir, "create_heatmap.R", sep="/");
17 source(heatmap_path); 17 source(heatmap_path);
18 18
19 if (opt$in_training_mode) { 19 if (opt$in_training_mode) {
20 ext <- ".para0"; 20 ext = ".para0";
21 para_files <- list.files(path=opt$input_dir, pattern="\\.para0$", full.names=TRUE); 21 pattern = "\\.para0$";
22 } else { 22 } else {
23 ext <- ".para"; 23 ext = ".para";
24 para_files <- list.files(path=opt$input_dir, pattern="\\.para$", full.names=TRUE); 24 pattern = "\\.para$"
25 } 25 }
26 para_files = list.files(path=opt$input_dir, pattern=pattern, full.names=TRUE);
26 for (i in 1:length(para_files)) { 27 for (i in 1:length(para_files)) {
27 para_file <- para_files[i]; 28 para_file = para_files[i];
28 para_file_base_name <- strsplit(para_file, split="/")[[1]][2]; 29 para_file_base_name = strsplit(para_file, split="/")[[1]][2];
29 output_file_base_name <- gsub(ext, "", para_file_base_name); 30 output_file_base_name = gsub(ext, "", para_file_base_name);
30 output_file_name <- paste(output_file_base_name, "state", i, "pdf", sep="."); 31 output_file_name = paste(output_file_base_name, "state", i, "pdf", sep=".");
31 output_file_path <- paste(opt$output_dir, output_file_name, sep="/"); 32 output_file_path = paste(opt$output_dir, output_file_name, sep="/");
32 data_frame <- read.table(para_file, comment="!", header=T); 33 data_frame = read.table(para_file, comment="!", header=T);
33 create_heatmap(data_frame, output_file_path); 34 create_heatmap(data_frame, output_file_path);
34 } 35 }