#!/usr/bin/env Rscript

suppressPackageStartupMessages(library("optparse"))

option_list <- list(
    make_option(c("--input_dir"), action="store", dest="input_dir", help="IDEAS para files directory"),
    make_option(c("--output_dir"), action="store", dest="output_dir", help="PDF output directory"),
    make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory")
)

parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
args <- parse_args(parser, positional_arguments=TRUE);
opt <- args$options;

heatmap_path <- paste(opt$script_dir, "create_heatmap.R", sep="/");
source(heatmap_path);

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);
}