--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_heatmaps.R	Wed Dec 20 11:24:23 2017 -0500
@@ -0,0 +1,25 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+
+option_list <- list(
+    make_option(c("-i", "--input_dir"), action="store", dest="input_dir", help="IDEAS para files directory"),
+    make_option(c("-o", "--output_dir"), action="store", dest="output_dir", help="PDF output directory")
+)
+
+parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
+args <- parse_args(parser, positional_arguments=TRUE);
+opt <- args$options;
+
+source("create_heatmap.R");
+
+para_files <- list.files(path=opt$input_dir, pattern="\\.para$", full.names=TRUE);
+for (i in 1:length(para_files)) {
+    para_file <- para_files[i];
+    para_file_base_name <- strsplit(para_file, split="/")[[1]][2];
+    output_file_base_name <- gsub(".para", "", para_file_base_name);
+    output_file_name <- paste(output_file_base_name, "state", i, "pdf", sep=".");
+    output_file_path <- paste(opt$output_dir, output_file_name, sep="/");
+    data_frame <- read.table(para_file, comment="!", header=T);
+    create_heatmap(data_frame, output_file_path);
+}