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

Jason Stajich jason at bioperl.org
Thu Oct 19 05:00:28 UTC 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?

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
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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

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