diff cluster.tools/remove.nulls.R @ 2:b442996b66ae draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/remove.nulls.R	Wed Feb 27 20:17:04 2013 -0500
@@ -0,0 +1,40 @@
+#!/usr/bin/env Rscript
+argspec <- c("remove.degenerate.values.R replaces degenerate values (NaNs & Infs) with a user-specified value
+
+        Usage: 
+                remove.degenerate.values.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 <- 'merge_merge.reals.tab' }
+
+mat <- as.matrix( read.delim( opt$data.fname, row.names=1, check.names=FALSE ) )
+cnames <-  sapply( strsplit( colnames( mat ), "\\s+" ), function(x) x[1] )
+colnames( mat ) <- cnames
+nulls <- mat[ , grepl( "^na", cnames ) ]
+reals <- mat[ , !grepl( "^na", cnames ) ]
+
+reals <- cbind( rownames( reals ), reals ); rownames( reals ) <- NULL
+reals <- rbind( colnames( reals ), reals ); colnames( reals ) <- NULL
+reals[1,1] <- "ID"
+write.table( reals, opt$output.fname, quote=FALSE, sep="\t", row.names=FALSE, col.names=FALSE )