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comparison build_matrix.R @ 22:f8e36f4b71c7 draft

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author greg
date Fri, 11 Aug 2017 09:39:53 -0400
parents 7e22d880e551
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21:7e22d880e551 22:f8e36f4b71c7
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 #data_table <- read.table(opt$input) 15 data_table <- read.table(opt$input)
16 #as.matrix(data_table) 16 as.matrix(data_table)
17 #status <- match(data_table[,3], missing) 17 status <- match(data_table[,3], missing)
18 #data_table[,3] <- paste(opt$work_dir, data_table[,1], ".", data_table[,2], ".bed.gz", sep="") 18 data_table[,3] <- paste(opt$work_dir, data_table[,1], ".", data_table[,2], ".bed.gz", sep="")
19 #data_table <- data_table[is.na(status)==TRUE,] 19 data_table <- data_table[is.na(status)==TRUE,]
20 #write.table(array(data_table, dim=c(length(data_table)/3, 3)), file=opt$output, quote=FALSE, row.names=FALSE, col.names=FALSE) 20 write.table(array(data_table, dim=c(length(data_table)/3, 3)), file=opt$output, quote=FALSE, row.names=FALSE, col.names=FALSE)
21
22 x=as.matrix(read.table(opt$input))
23 t=match(x[,3],missing)
24 x[,3]=paste(opt$work_dir, x[,1],".",x[,2],".bed.gz", sep="")
25 x=x[is.na(t)==T,]
26 write.table(array(x,dim=c(length(x)/3,3)), opt$output, quote=F,row.names=F,col.names=F)