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comparison create_heatmaps.R @ 143:269e7e466b00 draft

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Uploaded
author greg
date Wed, 20 Dec 2017 13:01:10 -0500
parents a976dd6fcd1b
children 08e77c105188
comparison
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142:8cfcf32c4282 143:269e7e466b00
1 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
2 2
3 suppressPackageStartupMessages(library("optparse")) 3 suppressPackageStartupMessages(library("optparse"))
4 4
5 option_list <- list( 5 option_list <- list(
6 make_option(c("-i", "--input_dir"), action="store", dest="input_dir", help="IDEAS para files directory"), 6 make_option(c("--input_dir"), action="store", dest="input_dir", help="IDEAS para files directory"),
7 make_option(c("-o", "--output_dir"), action="store", dest="output_dir", help="PDF output directory") 7 make_option(c("--output_dir"), action="store", dest="output_dir", help="PDF output directory"),
8 make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory")
8 ) 9 )
9 10
10 parser <- OptionParser(usage="%prog [options] file", option_list=option_list); 11 parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
11 args <- parse_args(parser, positional_arguments=TRUE); 12 args <- parse_args(parser, positional_arguments=TRUE);
12 opt <- args$options; 13 opt <- args$options;
13 14
14 source("create_heatmap.R"); 15 heatmap_path <- paste(opt$script_dir, "create_heatmap.R", sep="/");
16 source(heatmap_path);
15 17
16 para_files <- list.files(path=opt$input_dir, pattern="\\.para$", full.names=TRUE); 18 para_files <- list.files(path=opt$input_dir, pattern="\\.para$", full.names=TRUE);
17 for (i in 1:length(para_files)) { 19 for (i in 1:length(para_files)) {
18 para_file <- para_files[i]; 20 para_file <- para_files[i];
19 para_file_base_name <- strsplit(para_file, split="/")[[1]][2]; 21 para_file_base_name <- strsplit(para_file, split="/")[[1]][2];