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

Emmanuel Quevillon tuco at pasteur.fr
Wed Dec 16 10:37:45 EST 2009

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 
For my small problem I can keep this solution which far adapted for my 



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

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