diff cluster.tools/tab.2.cdt.R @ 0:0decf3fd54bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/tab.2.cdt.R	Thu Feb 28 01:45:39 2013 -0500
@@ -0,0 +1,43 @@
+#!/usr/bin/env Rscript
+argspec <- c("tab.2.cdt.R converts a data matrix to cdt format
+
+        Usage: 
+                tab.2.cdt.R -d <data.file> 
+        Optional:
+                            -o <output_file>
+                \n\n")
+args <- commandArgs(TRUE)
+if ( length( args ) == 1 && args =="--help") { 
+  write(argspec, stderr())
+  q();
+}
+
+
+lib.load.quiet <- function( package ) {
+   package <- as.character(substitute(package))
+   suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
+}
+lib.load.quiet(getopt)
+
+
+spec <- matrix( c( "data.fname",      "d", 1, "character",
+                   "output.fname",    "o", 2, "character"
+                   ),
+                nc=4,
+                byrow=TRUE
+               )
+
+opt <- getopt( spec=spec )
+if ( is.null( opt$output.fname ) ) opt$output.fname <- sub( "tab$|csv$", "cdt", opt$data.fname )
+
+data <- as.matrix( read.delim( opt$data.fname, row.names=1, check.names=FALSE ) )
+cnames <- colnames( data )
+data <- cbind( data[,1], data[,1], rep(1,nrow(data) ), data[, 2:ncol(data)] )
+data <- rbind( c( "EWEIGHT", "", NA,
+                  rep( 1, length( cnames[-1] ) ) ),
+               data )
+colnames( data ) <- c( "UNIQID", "NAME", "GWEIGHT", cnames[-1] )
+data <- rbind( colnames( data ), data )
+colnames( data ) <- NULL
+
+write.table( data, opt$output.fname, sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE )