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1 #!/usr/bin/env Rscript
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2
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3 suppressPackageStartupMessages(library("optparse"))
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4
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5 option_list <- list(
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6 make_option(c("--input_dir"), action="store", dest="input_dir", help="IDEAS para files directory"),
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7 make_option(c("--output_dir"), action="store", dest="output_dir", help="PDF output directory"),
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8 make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory"),
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9 make_option(c("--in_training_mode"), action="store_true", dest="in_training_mode", default=FALSE, help="Flag for training mode")
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10 )
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11
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12 parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
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13 args <- parse_args(parser, positional_arguments=TRUE);
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14 opt <- args$options;
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15
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16 heatmap_path = paste(opt$script_dir, "create_heatmap.R", sep="/");
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17 source(heatmap_path);
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18
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19 if (opt$in_training_mode) {
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20 ext = ".para0";
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21 pattern = "\\.para0$";
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22 } else {
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23 ext = ".para";
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24 pattern = "\\.para$"
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25 }
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26 para_files = list.files(path=opt$input_dir, pattern=pattern, full.names=TRUE);
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27 for (i in 1:length(para_files)) {
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28 para_file = para_files[i];
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29 para_file_base_name = strsplit(para_file, split="/")[[1]][2];
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30 output_file_base_name = gsub(ext, "", para_file_base_name);
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31 output_file_name = paste(output_file_base_name, "state", i, "pdf", sep=".");
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32 output_file_path = paste(opt$output_dir, output_file_name, sep="/");
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33 data_frame = read.table(para_file, comment="!", header=T);
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34 create_heatmap(data_frame, output_file_path);
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35 }
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