use Bio::FeatureIO::gff;
use Bio::SeqFeature::Annotated;
open($fh,"chr01_Canonical.gff3") or die "can't open file $!";
my $featureOut = Bio::FeatureIO->new(
-format => 'gff',
-version => 3,
-fh => $fh,
-validate_terms => 0, #boolean. validate ontology terms online? default 0 (false).
);
#@features= $featureOut->next_feature_group;
my @toplevel_features;
while (my @fg = $featureOut->next_feature_group) {
push(@toplevel_features, @fg);
}
print @toplevel_features;
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Parent with ID 13101.t00002 not found!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:368
STACK: Bio::FeatureIO::gff::next_feature_group /usr/lib/perl5/site_perl/5.10.0/Bio/FeatureIO/gff.pm:227
STACK: /home/vasilis/workspace/mrnaClean/gffParser.pl:15
-----------------------------------------------------------