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

Sendu Bala bix at sendu.me.uk
Fri Dec 1 13:52:44 EST 2006

Sendu Bala wrote:
> pelikan at cs.pitt.edu wrote:
>> 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?

In fact, if I just try and load it again I reproduce the problem.
The situation is similar to http://bugzilla.bioperl.org/show_bug.cgi?id=2092

And I have a tentative fix that extends Brian's fix there. Committed to 
HEAD only atm. I don't know anything about bioperl-db and don't have the 
faintest clue why this is happening, nor the time to figure it out. Can 
someone please have a proper look at this and decide if my fix is sane?

All I can say is the the test suites for bioperl-live and bioperl-db 
continue to pass, but that isn't really saying much.

PS. having used load_seqdatabase.pl to load a sequence, how do I remove 
it afterwards?

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