|
2
|
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"),
|
|
15
|
8 make_option(c("-w", "--work_dir"), action="store", dest="work_dir", help="Working directory"),
|
|
2
|
9 )
|
|
|
10
|
|
|
11 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
|
|
|
12 args <- parse_args(parser, positional_arguments=TRUE)
|
|
|
13 opt <- args$options
|
|
|
14
|
|
|
15 r_matrix = as.matrix(read.table(opt$input));
|
|
|
16 status = match(r_matrix[,3], missing);
|
|
13
|
17 r_matrix[,3] = paste(opt$work_dir, r_matrix[,1], ".", r_matrix[,2], ".bed.gz", sep="");
|
|
2
|
18 r_matrix = r_matrix[is.na(status)==T,];
|
|
|
19 write.table(array(r_matrix, dim = c(length(r_matrix) / 3, 3)), opt$output, quote=F, row.names=F, col.names=F);
|
