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comparison build_matrix.R @ 16:79acab9c6524 draft

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author greg
date Thu, 10 Aug 2017 14:41:35 -0400
parents 65739ddd00be
children e8dd7b5e4e95
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15:65739ddd00be 16:79acab9c6524
3 suppressPackageStartupMessages(library("optparse")) 3 suppressPackageStartupMessages(library("optparse"))
4 4
5 option_list <- list( 5 option_list <- list(
6 make_option(c("-i", "--input"), action="store", dest="input", help="Input .bed.gz file produced by prepMat"), 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"), 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"), 8 make_option(c("-w", "--work_dir"), action="store", dest="work_dir", help="Working directory")
9 ) 9 )
10 10
11 parser <- OptionParser(usage="%prog [options] file", option_list=option_list) 11 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
12 args <- parse_args(parser, positional_arguments=TRUE) 12 args <- parse_args(parser, positional_arguments=TRUE)
13 opt <- args$options 13 opt <- args$options
14 14
15 r_matrix = as.matrix(read.table(opt$input)); 15 r_matrix <- as.matrix(read.table(opt$input));
16 status = match(r_matrix[,3], missing); 16 status <- match(r_matrix[,3], missing);
17 r_matrix[,3] = paste(opt$work_dir, r_matrix[,1], ".", r_matrix[,2], ".bed.gz", sep=""); 17 r_matrix[,3] <- paste(opt$work_dir, r_matrix[,1], ".", r_matrix[,2], ".bed.gz", sep="");
18 r_matrix = r_matrix[is.na(status)==T,]; 18 r_matrix <- r_matrix[is.na(status)==T,];
19 write.table(array(r_matrix, dim = c(length(r_matrix) / 3, 3)), opt$output, quote=F, row.names=F, col.names=F); 19 write.table(array(r_matrix, dim=c(length(r_matrix)/3, 3)), opt$output, quote=F, row.names=F, col.names=F);