|
0
|
1 #!/usr/bin/env Rscript
|
|
|
2 argspec <- c("tab.2.cdt.R converts a data matrix to cdt format
|
|
|
3
|
|
|
4 Usage:
|
|
|
5 tab.2.cdt.R -d <data.file>
|
|
|
6 Optional:
|
|
|
7 -o <output_file>
|
|
|
8 \n\n")
|
|
|
9 args <- commandArgs(TRUE)
|
|
|
10 if ( length( args ) == 1 && args =="--help") {
|
|
|
11 write(argspec, stderr())
|
|
|
12 q();
|
|
|
13 }
|
|
|
14
|
|
|
15
|
|
|
16 lib.load.quiet <- function( package ) {
|
|
|
17 package <- as.character(substitute(package))
|
|
|
18 suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
|
|
|
19 }
|
|
|
20 lib.load.quiet(getopt)
|
|
|
21
|
|
|
22
|
|
|
23 spec <- matrix( c( "data.fname", "d", 1, "character",
|
|
|
24 "output.fname", "o", 2, "character"
|
|
|
25 ),
|
|
|
26 nc=4,
|
|
|
27 byrow=TRUE
|
|
|
28 )
|
|
|
29
|
|
|
30 opt <- getopt( spec=spec )
|
|
|
31 if ( is.null( opt$output.fname ) ) opt$output.fname <- sub( "tab$|csv$", "cdt", opt$data.fname )
|
|
|
32
|
|
|
33 data <- as.matrix( read.delim( opt$data.fname, row.names=1, check.names=FALSE ) )
|
|
|
34 cnames <- colnames( data )
|
|
|
35 data <- cbind( data[,1], data[,1], rep(1,nrow(data) ), data[, 2:ncol(data)] )
|
|
|
36 data <- rbind( c( "EWEIGHT", "", NA,
|
|
|
37 rep( 1, length( cnames[-1] ) ) ),
|
|
|
38 data )
|
|
|
39 colnames( data ) <- c( "UNIQID", "NAME", "GWEIGHT", cnames[-1] )
|
|
|
40 data <- rbind( colnames( data ), data )
|
|
|
41 colnames( data ) <- NULL
|
|
|
42
|
|
|
43 write.table( data, opt$output.fname, sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE )
|
