diff fingerprint.r @ 0:0cebe436a553 draft default tip

Initial upload.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fingerprint.r	Fri May 17 14:29:33 2013 -0400
@@ -0,0 +1,50 @@
+#!/usr/bin/env Rscript
+
+#sink(file("/dev/null", "w"), type = "message");
+
+library(affy)
+library(GEOquery);
+library(pathprint);
+
+# Figure out the relative path to the galaxy-pathprint.r library.
+script.args  <- commandArgs(trailingOnly = FALSE);
+script.name  <- sub("--file=", "", script.args[grep("--file=", script.args)])
+script.base  <- dirname(script.name)
+library.path <- file.path(script.base, "galaxy-pathprint.r");
+source(library.path)
+
+data(GEO.metadata.matrix);
+
+usage <- function() {
+  sink(stderr(), type = "message");
+  stop("Usage: fingerprint.r [ARGS]", call. = FALSE)
+}
+
+## Get the command line arguments.
+args <- commandArgs(trailingOnly = TRUE)
+
+type <- ifelse(! is.na(args[1]), args[1], usage())
+
+if (type == "geo") {
+   geoID       <- ifelse(! is.na(args[2]), args[2], usage());
+   output      <- ifelse(! is.na(args[3]), args[3], usage());
+
+   fingerprint <- generateFingerprint(geoID);
+} else if (type == "cel") {
+   input       <- ifelse(! is.na(args[2]), args[2], usage());
+   output      <- ifelse(! is.na(args[3]), args[3], usage());
+
+   fingerprint <- loadFingerprintFromCELFile(input);
+} else if (type == "expr") {
+   input       <- ifelse(! is.na(args[2]), args[2], usage());
+   platform    <- ifelse(! is.na(args[3]), args[3], usage());
+   output      <- ifelse(! is.na(args[4]), args[4], usage());
+
+   fingerprint <- loadFingerprintFromExprsFile(input, platform);
+} else {
+  usage();
+};
+
+saveFingerprint(fingerprint, output);
+
+quit("no", 0)