diff GALAXY_FILES/tools/EMBER/Expression_Pattern_Distance.pl @ 0:003f802d4c7d

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GALAXY_FILES/tools/EMBER/Expression_Pattern_Distance.pl	Wed Feb 29 15:03:33 2012 -0500
@@ -0,0 +1,73 @@
+#!/usr/bin/perl
+# computes difference distances between motif models
+
+if( $#ARGV != 1 ){
+	print "Usage: ./Expression_Pattern_Distance.pl model1 model2\n";
+	exit;
+}
+
+@model1 = &read_model( $ARGV[0] );
+@model2 = &read_model( $ARGV[1] );
+if( $#model1 != $#model2 ){
+	print "Error: model dimensions do not match\n";
+	exit;
+}
+
+
+#
+# second distance: sum of absolute difference, divided by absolute sum
+# bounded between 0 and 1; equals 1 if all signs are different
+#
+$dist = 0;
+$denom = 0;
+for($i=0; $i< $classes; $i++){
+	for($j=0; $j< $dims; $j++){
+		if( $model1[$i][$j] ne "nan" && $model2[$i][$j] ne "nan" ){
+			$dist+= abs($model1[$i][$j] - $model2[$i][$j]);
+			$denom+= abs($model1[$i][$j]) + abs($model2[$i][$j]);
+		}
+	}
+}
+$dist/=$denom;
+
+printf("%0.3f\n", $dist);
+
+
+exit;
+
+
+
+
+################################
+
+# function to read a motif model from file $_[0]
+sub read_model{
+	$dims = 0;
+	$classes = 0;
+	open(IN,"$_[0]") || die "Error: can't open file $_[0]\n";
+	@modpars = ();
+	# burn the first two lines
+	$line = <IN>;
+	$line = <IN>;
+	while( $line = <IN> ){
+		chomp($line);
+		@parts = split(' ',$line);
+		if($parts[0] !~ /#/ ){
+			@parts2 = ();
+			for($i=1; $i<= $#parts; $i++){
+				if( $parts[$i] ne "NA" ){
+					push(@parts2, $parts[$i]);
+				}
+				else{
+					push(@parts2, 0);
+				}
+			}
+			push(@modpars, [@parts2] );
+			$classes++;
+			$dims = $#parts;
+		}
+	}
+	close(IN);
+	return @modpars;
+}
+