[Bioperl-l] Data missing into Annotation object using Bio::SeqIO (Genbank)
Emmanuel Quevillon
tuco at pasteur.fr
Wed Dec 16 14:14:28 UTC 2009
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
-------------------------
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