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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/remove.degenerate.values.R	Wed Feb 27 20:17:04 2013 -0500
@@ -0,0 +1,41 @@
+#!/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:
+                                           -r <replacement_value> (default is NA)
+                                           -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",
+                   "replacement.val", "r", 2, "character",
+                   "output.fname",    "o", 2, "character"
+                   ),
+                nc=4,
+                byrow=TRUE
+               )
+
+opt <- getopt( spec=spec )
+
+data <- as.matrix( read.delim( opt$data.fname, row.names=1, check.names=FALSE ) )
+if ( is.null( opt$replacement.val ) ) { opt$replacement.val <- NA }
+if ( ! is.null( opt$replacement.val ) ) { opt$replacement.val <- as.integer( opt$replacement.val ) }
+if ( is.null( opt$output.fname ) ) { opt$output.fname <- paste( "degenerate.vals.replaced", basename( opt$data.fname ), sep="." ) }
+
+## Set any NA, NAN or Inf entries to 0
+if ( any(is.nan(data)) ) data[ is.nan( data ) ] <- opt$replacement.val
+if ( any(is.infinite(data)) ) data[ is.infinite( data ) ] <- opt$replacement.val
+
+write.table( data, opt$output.fname, sep="\t", quote=FALSE, col.names=NA )