[Bioperl-l] Fwd: problem with bioperl (where's the Mus?)

[Chris Fields]

On Aug 24, 2009, at 2:12 PM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>> On Aug 24, 2009, at 1:16 PM, Sendu Bala wrote:
>>>> This points to a problem in Bio::Species::scientific_name(),  
>>>> given that binomial() is correct. Could you file this as a bug  
>>>> report?
>>>
>>> What code creates the Bio::Species object here? I suspect this  
>>> code isn't aware of changes in Bio::Species since BioPerl 1.5.2.
>> I see. Any pointer to what would tell me what I need to change or  
>> is everything in the Bio::Species POD?
>
> ... I won't guarantee the perfection of the POD ;)
>
>
>> BTW what the Bioperl-db code does is instantiate the blank object  
>> and then populate it through its accessors (mostly the  
>> classification() array). If what it has been doing in the past is  
>> now considered incorrect, at least it doesn't raise any warning  
>> that would alert one to that ...
>
> Yuh... If you point out the code that creates the Bio::Species I can  
> look into it for you and suggest what needs changing and why it  
> doesn't work (or if it's a bug in Bio::Species). I can't remember  
> things clearly right now, though classification() I guess was  
> supposed to be backwards compatible.

Sendu, I think it's related to this:

http://bugzilla.open-bio.org/show_bug.cgi?id=2092#c4

Bio::DB::BioSQL::SpeciesAdaptor and  
Bio::DB::BioSQL::mysql::SpeciesAdaptorDriver are the two modules in  
question i think.

chris