[Bioperl-l] load_seqdatabase.pl error

Sendu Bala bix at sendu.me.uk
Thu Sep 27 04:38:00 EDT 2007


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?


More information about the Bioperl-l mailing list