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

[Emmanuel Quevillon]

On 12/16/2009 04:09 PM, Chris Fields wrote:
> 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
>
>    
Hi Chris

Thanks for the infos.
I indeed revert back to using $feat->get_tag_values() and it works as 
previously.
For my small problem I can keep this solution which far adapted for my 
problem.

Regards

Emmanuel

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