[Bioperl-l] Error with supplied lineages importing uniprot data

Sendu Bala bix at sendu.me.uk
Fri Dec 1 12:12:49 EST 2006


pelikan at cs.pitt.edu wrote:
> Hello all,
> 
>  I'm running bioperl 1.5.2, bioperl-db 1.5.2 - RC005, under windows,
> without Cygwin. The "make test"s have all completed without error. This
> is my first time dealing with bioperl, so bear with me.
> 
>    I've successfully loaded the most recent taxonomy information using the
> biosql-schema scripts. After this, I attempted to load the most recent
> release of the uniprot flat file dataset with the following command:
> 
> load_seqdatabase.pl -drive mysql -dbname bioseqdb -dbuser root -dbpass
> ********* -format swiss -safe c:\data\uniprot\uniprot_sprot.dat
> 
> I am subsequently greeted by many of the following errors:
> 
> Could not store Q7N3Q6:

I extracted just Q7N3Q6 from 
ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz
and was able to load it in using load_seqdatabase.pl under linux with no 
errors. If you make a file with just that sequence do you still get the 
error?

Is anyone else able to reproduce the problem?


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