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comparison build_matrix.R @ 2:7a77ec6342c1 draft

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author greg
date Thu, 10 Aug 2017 12:34:42 -0400
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children c59cbd44dcff
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1:d75cbb2db2c4 2:7a77ec6342c1
1 #!/usr/bin/env Rscript
2
3 suppressPackageStartupMessages(library("optparse"))
4
5 option_list <- list(
6 make_option(c("-i", "--input"), action="store", dest="input", help="Input .bed.gz file produced by prepMat"),
7 make_option(c("-o", "--output"), action="store", dest="output", help="Output file"),
8 make_option(c("-w", "--work_dir"), action="store", dest="work_dir", help="Working directory"),
9 )
10
11 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
12 args <- parse_args(parser, positional_arguments=TRUE)
13 opt <- args$options
14
15 input_dir = paste(opt$work_dir, "Input/", sep="");
16 r_matrix = as.matrix(read.table(opt$input));
17 status = match(r_matrix[,3], missing);
18 r_matrix[,3] = paste(input_dir, r_matrix[,1], ".", r_matrix[,2], ".bed.gz", sep="");
19 r_matrix = r_matrix[is.na(status)==T,];
20 write.table(array(r_matrix, dim = c(length(r_matrix) / 3, 3)), opt$output, quote=F, row.names=F, col.names=F);