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

[Sendu Bala]

Chris Fields wrote:
> 
> 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.

Ah, yes, well there you go then. So it is a classification() issue. 
Judging by what I said in that bug, looks like the db code needs to be 
changed to put the full scientific name in the first element it passes 
to classification.