[Bioperl-l] load_seqdatabase.pl error

[Chris Fields]

On Sep 27, 2007, at 3:38 AM, Sendu Bala wrote:

> Forrest wrote:
>> Hi, all
>>     I install the biosql, and bioperl-db. I want to import  
>> swissport data.
>> But the programe show some error as below:
>> ===================================================================== 
>> =======
>> ===============================================
>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver mysql
>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>> Could not store Q6DAH5:
>> ------------- EXCEPTION: Bio::Root::Exception -------------
>> MSG: The supplied lineage does not start near 'Erwinia carotovora  
>> subsp.
>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |  
>> Pectobacterium |
>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>> Proteobacteria | Bacteria')
>
> From:
> OS   Erwinia carotovora subsp. atroseptica (Pectobacterium  
> atrosepticum).
> OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
> OC   Enterobacteriaceae; Pectobacterium.
>
> I'm guessing some oddity in the Swissprot parser where in one place it
> truncates the OS to the first '.', and in another it doesn't?
>
> Can someone confirm this with CVS versions of bioperl-live and -db in
> case Chris already fixed it in recent parser changes?

It looks suspiciously like he isn't using bioperl-live code (I  
changed the exception to a warning a while back, and I think the '.'  
truncation was fixed).  This is still an outstanding issue with  
bioperl-db which hasn't been fully fixed yet, though; we may have to  
move the priority up on this one.

chris