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

[Chris Fields]

On Aug 24, 2009, at 10:17 PM, Hilmar Lapp wrote:

>
> On Aug 24, 2009, at 4:27 PM, Chris Fields wrote:
>
>>
>> On Aug 24, 2009, at 3:01 PM, Sendu Bala wrote:
>>
>>> [...]
>>> 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.
>>
>>
>> Yup.  I believe the only blocking issue with implementing it was  
>> potential backwards-compat problems with databases loaded using old  
>> behavior and then being updated post-1.5.2 (new behavior).
>
> The code change is for retrieving data, right? So I'm not sure how  
> it would break backwards compatibility, unless one has taxon entries  
> created before the change (i.e., about 3 years ago?) and through  
> loading sequences rather than through loading the NCBI taxonomy.
>
> 	-hilmar

Okay, if possible I would like you or Sendu to review that last commit  
I made to bioperl-db.  It includes Sendu's patch; I commented out  
sections that were modifying the genus/species when loaded in, but  
there are a few TODO's I noted as well (everything is in  
populate_from_row()).

02species.t is now failing but I think it's based on the same old  
behavior; I'll look into it.

chris