[Bioperl-l] Re: Handling gff3 Target and Dbxref tags through FeatureIO

Allen Day allenday at ucla.edu
Wed Oct 20 18:47:41 EDT 2004

Dbxref tags - these can be added to the AnnotationCollection as
Bio::Annotation::DBLink objects.  These are already being created, but due
to oversight on my part not attached.  The code fragment below illustrates
this.  Just add a few lines to add them to the Collection and voila!

  #Handle Dbxref attributes
    foreach my $value (@{ $attr{Dbxref} }){
      my $a = Bio::Annotation::DBLink->new();
      my($db,$accession) = $value =~ /^(.+?):(.+)$/;

      if(!$db or !$accession){ #dbxref malformed
        $self->throw("Error in line:\n$feature_string\nDbxref value 
'$value' did not conform to GFF3 specification");


Target tags - Bio::SeqFeature::Annotated needs to be able to have
Bio::LocatableSeq or Bio::Location::Simple attachments.  Presumably you
can have multiple targets.  Do something like create methods
add_location() and locations() methods.


On Wed, 20 Oct 2004, Scott Cain wrote:

> Hi Allen,
> I am in fairly urgent need of the ability to handle Target and Dbxref
> tags in GFF3, as I need to add that ability to the chado GFF3 bulk
> loader.  Can you give me some guidance on what I need to do?
> Thanks,
> Scott

More information about the Bioperl-l mailing list