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

[Anand C. Patel]

I preloaded the NCBI taxonomy into the biosql database using the  
provided script before adding the sequences from genbank format text  
file (downloaded directly from genbank) using the script provided by  
bioperl-db, which would be what created the Bio::Species objects (I'd  
assume) from the text files, prior to inserting them into the database.

Hope this helps,
Anand

On Aug 24, 2009, at 3:27 PM, Chris Fields wrote:

>
> On Aug 24, 2009, at 3:01 PM, Sendu Bala wrote:
>
>> 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.
>
>
> 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).  I would  
> think this only affects sequence data loaded w/o taxonomy preloaded,  
> but I'm not sure.
>
> I suggest, if you can fix it, go ahead make the necessary change.   
> We can then post a big warning to BioSQL and here about the problem,  
> something along the lines of 'bioperl-db in svn may be backwards  
> incompatible with species information loaded in previous versions;  
> it may eat your first born' or similar.  It's an absolutely  
> necessary fix, and may effectively kill a bunch of other db/species- 
> related bugs.
>
> chris
>