[Bioperl-l] Bio::DB::BioDB - insert failed. Dupllicate entry ''for key 2?

Marc Logghe Marc.Logghe at DEVGEN.com
Sun Mar 5 09:26:26 EST 2006


Hi Jay,
Yes, I agree with Chris. I also think you'd be better off with
load_seqdatabase.pl.

> >
> > At this point I can see my first sequence loaded into mySQL.  
> > biodatabase and biosequence have stuff in them. e.g.:
> >
> >
> > mysql> select * from biodatabase;
> > +----------------+------+-----------+-------------+
> > | biodatabase_id | name | authority | description |
> > +----------------+------+-----------+-------------+
> > |             23 |      | NULL      | NULL        |
> > +----------------+------+-----------+-------------+
> > 1 row in set (0.00 sec)
> >
> >
> >
> > And I noticed that if I delete that sequence from the database, I  
> > can once again load it, and the number biodatabase_id (23)  
> > increments. 20, 21, 22, 23, etc.

BTW, here you actually did not delete your sequence but the namespace.
If you want to check 'sequences' you should look into the bioentry
table.

Using load_seqdatabase.pl the namespace is set automatically to the
default ('bioperl') but you can set it as well with the --namespace
option.

HTH,
Marc



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