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

[Sendu Bala]

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.