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

Jason Stajich jason at bioperl.org
Thu Oct 19 11:50:49 EDT 2006


Well there is explicit addition of the version to the primary id so  
it isn't so much a parsing error as a deliberate decision to append it.
see Bio::SeqIO::genbank

to make the dblink
                                               $annotation- 
 >add_Annotation
                                                     ('dblink',
                                                       
Bio::Annotation::DBLink->new
                                                      (-primary_id =>  
$id . "." . $version,
                                                       -version =>  
$version,
                                                       -database => $db,
                                                       -tagname =>  
'dblink'));

and the code to print the dblink back out in the writer already  
assumes the version number is appended...

         foreach my $ref ( $seq->annotation->get_Annotations 
('dblink') ) {
             # if ($ref->comment eq 'DBSOURCE') {
             $self->_print('DBSOURCE    accession ',
                           $ref->primary_id, "\n");
             # }
         }

On Oct 19, 2006, at 6:56 AM, Hilmar Lapp wrote:

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

--
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




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