[Bioperl-l] Two Bio::DB::Flat swiss adaptors

Brian Osborne bosborne11 at verizon.net
Wed Mar 21 12:23:22 EDT 2007


Chris,

"swiss" is presumably the preferred name since this is what is used over in
SeqIO.

Brian O.


On 3/21/07 12:19 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:

> That's what I am thinking as well.  I may try removing the one with
> the version error to see what happens with tests...
> 
> chris
> 
> On Mar 21, 2007, at 10:59 AM, Hilmar Lapp wrote:
> 
>> Maybe someone wanted to change the name and failed to remove the
>> original?
>> 
>> On Mar 21, 2007, at 12:34 AM, Chris Fields wrote:
>> 
>>> Just curious, but why are there two Bio::DB::Flat::BDB swissprot
>>> adaptors (Bio::DB::Flat::BDB::swiss, Bio::DB::Flat::BDB::swissprot)?
>>> The only significant difference between the two is the following line
>>> in seq_to_ids():
>>> 
>>> Bio::DB::Flat::BDB::swiss : $ids{VERSION}  = "$accession.$version"
>>> if defined $accession && defined $version;
>>> Bio::DB::Flat::BDB::swiss : $ids{VERSION}  = "$accession.version"
>>> if defined $accession && defined $version;
>>> 
>>> The second is missing '$' in version, which I'm guessing is a bug?
>>> 
>>> chris
>>> 
>>> _______________________________________________
>>> 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 :
>> ===========================================================
>> 
>> 
>> 
>> 
>> 
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
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