[Bioperl-l] Annotation-DBLink- version numbers repeating

Chris Fields cjfields at uiuc.edu
Tue Oct 17 16:30:15 EDT 2006


I can confirm this using bioperl-live:

GenBank:AL591065.17.17
/Users/cjfields/src/bioperl-live/Bio/Annotation/DBLink.pm

Could you file a bug report via bugzilla?

Chris

On Oct 17, 2006, at 2:01 PM, Erikjan wrote:

> Hello,
>
> I noticed a little problem with the Annotation "DBLink" from  
> GenBank entries
>
> When I run:
>
> perl -MBio::DB::GenBank -e 'my $gi =
> 56205924;$db=Bio::DB::GenBank->new(-format => "genbank"); my $seqio =
> $db->get_Stream_by_id($gi); my$seq = $seqio->next_seq; my
> $ac=$seq->annotation(); my @annotations = $ac->get_Annotations 
> ("dblink");
> for(@annotations) { print $_, "\n";} print $INC{
> "Bio/Annotation/DBLink.pm" }, "\n"; '
>
> This yields:
>
>    GenBank:AL591065.17.17
>
> and the place where the used Bio/Annotation/DBLink.pm resides.
>
> Can others repeat this?
>
> I have dug into the source a little and Bio::Annotation::DBLink  
> seems to
> be the place where this happens: it has a concatenation which leads to
> that repeated version number.
>
> It this something that I should fix "client-side", so to speak, or  
> is it
> worthwhile to add some logic to that concatenation to prevent this?
>
>
> Thanks,
>
> Eric
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list