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

Jason Stajich jason at bioperl.org
Thu Oct 19 01:00:28 EDT 2006


So I'm unsure what we should do here.

We can certainly fix the problem which you report which is relying on  
the "" method -- if you were to do instead:
print $_->database, ":", $_->primary_id, "\n";

you'll get the right answer.  We at a minimum just fix the auto- 
string converting method to do The Right Thing.

But I am not sure if we should keep the version out of the primary_id  
field.  This will require some rejiggering in several modules when it  
comes to printing DBlinks and I don't want to do this before the  
release. I also am not sure if there was an explicit reason why  
someone did put the version information in the primary_id. (I hope it  
wasn't me because I don't think I'm going to remember why).

Does anyone else have a strong feeling?

-jason
On Oct 17, 2006, at 12:01 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

--
Jason Stajich, PhD
Miller Research Fellow
University of California
Dept of Plant and Microbial Biology
321 Koshland Hall #3102
Berkeley, CA 94720-3102
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html




More information about the Bioperl-l mailing list