[Bioperl-l] Annotation object problem

[Jason Stajich]

Without sending us code can't give you the exact changes you need but
basically you are using an old annotation interface - basically you need
to change your calls to do this:

my $annot = $seq->annotation();
# get the refences
foreach my $ref ( $annot->get_Annotations('reference') ) { .. }

foreach my $comm ( $annot->get_Annotations('comment) ) { .. }

Instead of:
foreach my $ref ( $annot->each_Reference() ) { .. }

foreach my $com ( $annot->each_Comment() ) { .. }

etc...

-jason
On Sun, 29 Sep 2002, Michael Muratet wrote:

> Greetings
>
> I am using Bioperl 1.0.1 on a file I just now downloaded from Genbank. I
> am trying to extact the annotation data, and I get the following errors:
>
> Using old style annotation call on new Annotation::Collection object
> STACK Bio::Annotation::Collection::description
> /usr/lib/perl5/site_perl/5.6.1/Bio/Annotation/Collection.pm:258
> STACK toplevel ./processGenbank.pl:12
> each_Reference (old style Annotation) on new style
> Annotation::Collection
> STACK Bio::Annotation::Collection::each_Reference
> /usr/lib/perl5/site_perl/5.6.1/Bio/Annotation/Collection.pm:360
> STACK toplevel ./processGenbank.pl:13
> each_Comment (old style Annotation) on new style Annotation::Collection
> STACK Bio::Annotation::Collection::each_Comment
> /usr/lib/perl5/site_perl/5.6.1/Bio/Annotation/Collection.pm:402
> STACK toplevel ./processGenbank.pl:14
> each_DBLink (old style Annotation) on new style Annotation::Collection
> STACK Bio::Annotation::Collection::each_DBLink
> /usr/lib/perl5/site_perl/5.6.1/Bio/Annotation/Collection.pm:445
> STACK toplevel ./processGenbank.pl:15
> id
>
>
> Is it trying to tell me that my bioperl is old style, or that the
> Genbank file is old style?
>
> Thanks.
>
> Mike
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu