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

[Chris Fields]

Emmanuel,

The previous behavior in the 1.5.x series was to store feature tags as Bio::Annotation.  The problem had been the way this was implemented was considered unsatisfactory for various reasons, so we reverted back to using simple tag-value pairs as the default.  You can get at the data this way (from the Feature/Annotation HOWTO):

for my $feat_object ($seq_object->get_SeqFeatures) {
    print "primary tag: ", $feat_object->primary_tag, "\n";
    for my $tag ($feat_object->get_all_tags) {
        print "  tag: ", $tag, "\n";
        for my $value ($feat_object->get_tag_values($tag)) {
            print "    value: ", $value, "\n";
        }   
    }
}

You can also convert all the tag-value data into a Bio::Annotation::Collection using the Bio::SeqFeature::AnnotationAdaptor, but this is completely optional.

chris

On Dec 16, 2009, at 8:14 AM, Emmanuel Quevillon wrote:

> 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
> -------------------------
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l