##source :  http://seqanswers.com/forums/showthread.php?t=15060
##01/12/2014 
##usage : perl sm_gff_to_gtf.ly myFile.gff > myFile.gtf
    
##!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

use File::Basename;
use Bio::FeatureIO;

my $inFile = shift;
my ($name, $path, $suffix) = fileparse($inFile, qr/\.gff/);
my $outFile = $path . $name . ".gtf";

my $inGFF = Bio::FeatureIO->new( '-file' => "$inFile",
'-format' => 'GFF',
'-version' => 3 );
my $outGTF = Bio::FeatureIO->new( '-file' => ">$outFile",
'-format' => 'GFF',
'-version' => 2.5);

while (my $feature = $inGFF->next_feature() ) {

$outGTF->write_feature($feature);

}