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141
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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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145
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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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141
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9 )
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10
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11 parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
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12 args <- parse_args(parser, positional_arguments=TRUE);
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13 opt <- args$options;
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14
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143
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15 heatmap_path <- paste(opt$script_dir, "create_heatmap.R", sep="/");
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16 source(heatmap_path);
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141
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17
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18 para_files <- list.files(path=opt$input_dir, pattern="\\.para$", full.names=TRUE);
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19 for (i in 1:length(para_files)) {
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20 para_file <- para_files[i];
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21 para_file_base_name <- strsplit(para_file, split="/")[[1]][2];
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22 output_file_base_name <- gsub(".para", "", para_file_base_name);
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23 output_file_name <- paste(output_file_base_name, "state", i, "pdf", sep=".");
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24 output_file_path <- paste(opt$output_dir, output_file_name, sep="/");
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25 data_frame <- read.table(para_file, comment="!", header=T);
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26 create_heatmap(data_frame, output_file_path);
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27 }
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