[Bioperl-l] Data missing into Annotation object using Bio::SeqIO (Genbank)

[Emmanuel Quevillon]

Hi,

I've wrote a small Genbank parser few months ago before BioPerl release 
1.6.0.
I tried to use my code once again but now the output of my parser is empty.
It looks like Annotation from seqfeatures is not filled anymore.

Here is the code I used previously:

while(my $seq = $streamer->next_seq()){

     #We only want to retrieve CDS features...
     foreach my $feat (grep { $_->primary_tag() eq 'CDS' } 
$seq->get_SeqFeatures()){
         print $ofh join("#",
                         
$feat->annotation()->get_Annotations('locus_tag'),    # Acc num
                         $feat->annotation()->get_Annotations('gene')
                           ? 
$feat->annotation()->get_Annotations('gene')      # Gene name
                           : 
$feat->annotation()->get_Annotations('locus_tag'),
                         
$feat->annotation()->get_Annotations('product'),      # Description
                        ),"\n";
     }
}

$feat is a Bio::SeqFeature::Generic object

If I print Dumper($feat->annotation()) here is the output :

$VAR1 = bless( {
                  '_typemap' => bless( {
                                         '_type' => {
                                                      'comment' => 
'Bio::Annotation::Comment',
                                                      'reference' => 
'Bio::Annotation::Reference',
                                                      'dblink' => 
'Bio::Annotation::DBLink'
                                                    }
                                       }, 'Bio::Annotation::TypeManager' ),
                  '_annotation' => {}
                }, 'Bio::Annotation::Collection' );

Have some changes been made into the way annotation object is populated?

Thanks for any clue and sorry if my question look stupid

Regards

Emmanuel

-- 
-------------------------
Emmanuel Quevillon
Biological Software and Databases Group
Institut Pasteur
+33 1 44 38 95 98
tuco at_ pasteur dot fr
-------------------------