#!/usr/bin/perl
# Peter Hallin 2007-02-06, to be used with RNAmmer v1.2

use XML::Simple;
use strict;

sub err {
	print "$_\n";
	exit 1;
}

# create object
my $xml = new XML::Simple (ForceArray => 1);

# read XML file
my $data = $xml->XMLin($ARGV[0]) or err ("error loading input:$!");

print  "##gff-version2\n";
print  "##source-version $data->{predictor}[0]\n";
print  "##date $data->{predictionDate}[0]\n";
print  "##Type DNA\n";
print  "# seqname           source                      feature     start      end   score   +/-  frame  attribute\n";
print  "# ---------------------------------------------------------------------------------------------------------\n";
foreach my $entry (@{$data->{entries}[0]->{entry}}) {
	next if defined $entry->{sequenceEntry}[0] eq "";
	print  ( join ("\t" , (
		$entry->{sequenceEntry}[0],
		$data->{predictor}[0],
		'rRNA',
		$entry->{start}[0],
		$entry->{stop}[0],
		$entry->{score}[0],
		$entry->{direction}[0],
		'.',
		$entry->{mol}[0],
		"\n"
	)));
}
print  "# ---------------------------------------------------------------------------------------------------------\n";