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

Hilmar Lapp hlapp at gmx.net
Thu Oct 19 09:56:05 EDT 2006


Here is the overload code:

use overload '""' => sub {
	(($_[0]->database ? $_[0]->database . ':' : '' )
	. ($_[0]->primary_id ? $_[0]->primary_id : '')
	. ($_[0]->version ? '.' . $_[0]->version : ''))
	|| '' };

Except that the last '||' is redundant and unnecessary (it either  
does nothing or replaces an empty string with an empty string), I  
don't see the potential for duplicating the version number here -  
unless primary_id() did that, which I don't see it doing.

So, to me this seems to come from a parsing error in the beginning,  
rather than an erroneous mangling of version into primary_id later.

Is someone in the position to confirm this?

	-hilmar

On Oct 19, 2006, at 1:00 AM, Jason Stajich wrote:

> 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
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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