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

Chris Fields cjfields at uiuc.edu
Wed Mar 21 12:34:42 EDT 2007


Yes, I agree.  The potential error with $version is actually in the  
'swissprot' version.  flat.t tests only use 'swiss' so I'm presuming  
that's the keeper.

chris

On Mar 21, 2007, at 11:23 AM, Brian Osborne wrote:

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

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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