--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_2_1a/snpEff_2_1a/scripts/data/rice5/mRnaAddParent.pl	Fri Apr 20 11:22:59 2012 -0400
@@ -0,0 +1,28 @@
+#!/usr/bin/perl
+
+#-------------------------------------------------------------------------------
+# Add 'Parent' option in mRNA lines
+#
+# 								Pablo Cingolani
+#-------------------------------------------------------------------------------
+
+while( $l = <STDIN> ) {
+	chomp $l;
+	@t = split /\t/,$l;
+
+	$type = $t[2];
+
+	# Is it an mRNA?
+	if( $type eq 'mRNA' ) {
+		# Parse ID in options 
+		$opts = $t[8];
+		if( $opts =~ /ID=(.*?)-\d+;/ ) {
+			$pid = $1;
+			$pid =~ tr/t/g/;
+			# Add 'Parent' option
+			$l .= ";Parent=$pid";
+		}
+	}
+
+	print "$l\n";
+}