--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Wig_to_bedGraph/script/wig2bedGraph_converter.pl	Tue Jun 07 18:08:31 2011 -0400
@@ -0,0 +1,62 @@
+#!/usr/bin/env perl
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# Written (W) 2010 Vipin T. Sreedharan, Friedrich Miescher Laboratory of the Max Planck Society
+# Copyright (C) 2010 Max Planck Society
+#
+# Description: - read fixedStep and variableStep wiggle input data,
+#		output four column bedGraph format data
+
+use warnings;
+use strict;
+
+my ($position, $chr, $step, $span) = (0, "", 1, 1);
+
+my $usage = q(
+fixedStep2BED.pl  - Program to convert a valid fixedStep or variableStep wiggle input data to BED format.
+USAGE: wig2bedGraph_converter <fixedStep/variableStep Wiggle format> > <output file name>
+
+);
+if (scalar(@ARGV) != 1) {
+    print $usage;
+    exit
+}
+
+my $inFile = $ARGV[0];
+open WIG, "<$inFile" || die "Can't open the Wiggle file \n";
+while (my $dataValue = <WIG>)
+{
+    chomp $dataValue;
+    next if ( $dataValue =~ m/^track /);
+    if ( $dataValue =~ m/^fixedStep/ || $dataValue =~ m/^variableStep/ ) {
+        ($position, $chr, $step, $span) = (0, "", 1, 1);
+        my @a = split('\s', $dataValue);
+        for (my $i = 1; $i < scalar(@a); ++$i) {
+            my ($ident, $value) = split('=',$a[$i]);
+            if ($ident =~ m/chrom/) { $chr = $value; }
+            elsif ($ident =~ m/start/) { $position = $value-1; }
+            elsif ($ident =~ m/step/) { $step = $value; }
+            elsif ($ident =~ m/span/) { $span = $value; }
+            else {
+                print STDERR "ERROR: unrecognized fixedStep/variableStep line: $dataValue\n";
+                exit 255;
+            }
+        }
+    } 
+    else {
+        my @b = split('\s', $dataValue);
+        if (scalar(@b)>1) {
+            $position = $b[0];
+            $dataValue = $b[1];
+        }
+        my $loc_pos = $position+$span;
+        print "$chr\t$position\t$loc_pos\t$dataValue\n";
+        $position = $position + $step;
+    }
+}
+close WIG;
+exit;