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comparison build_matrix.R @ 19:50f64f662726 draft

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Uploaded
author greg
date Fri, 11 Aug 2017 08:39:56 -0400
parents 54ec2ba55b87
children 7e22d880e551
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18:54ec2ba55b87 19:50f64f662726
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$input)); 15 data_table <- read.table(opt$input)
16 status <- match(r_matrix[,3], missing); 16 as.matrix(data_table)
17 r_matrix[,3] <- paste(opt$work_dir, r_matrix[,1], ".", r_matrix[,2], ".bed.gz", sep=""); 17 status <- match(data_table[,3], missing)
18 r_matrix <- r_matrix[is.na(status)==TRUE,]; 18 data_table[,3] <- paste(opt$work_dir, data_table[,1], ".", data_table[,2], ".bed.gz", sep="")
19 write.table(array(r_matrix, dim=c(length(r_matrix)/3, 3)), file=opt$output, quote=FALSE, row.names=FALSE, col.names=FALSE); 19 data_table <- data_table[is.na(status)==TRUE,]
20 write.table(array(data_table, dim=c(length(data_table)/3, 3)), file=opt$output, quote=FALSE, row.names=FALSE, col.names=FALSE)