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

Emmanuel Quevillon tuco at pasteur.fr
Wed Dec 16 09:14:28 EST 2009


I've wrote a small Genbank parser few months ago before BioPerl release 
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' } 
         print $ofh join("#",
$feat->annotation()->get_Annotations('locus_tag'),    # Acc num
$feat->annotation()->get_Annotations('gene')      # Gene name
$feat->annotation()->get_Annotations('product'),      # Description

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

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

$VAR1 = bless( {
                  '_typemap' => bless( {
                                         '_type' => {
                                                      'comment' => 
                                                      'reference' => 
                                                      '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



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

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