[Bioperl-l] loading data to biosql tables

[Angshu Kar]

Hi Hilmar,

In the load_seqdatabase.pl script could you please tell me where you are
inserting the data into the db tables, so that I can try and modify that
part to insert data only to the tables that I need ?

Thanks,
Angshu


On 12/8/05, Hilmar Lapp <hlapp at gmx.net> wrote:
>
> Any reason you didn't instantiate the rest of the schema? Any scripts
> and software that have been written against BioSQL will certainly
> expect the rest of the schema be present ...
>
> Bioperl-db is the BioSQL language binding for Bioperl, so that's what
> you will want to use. It comes with a script load_seqdatabase.pl to
> load any format supported by Bioperl.
>
> However, bioperl-db does expect all of Biosql to be present ...
>
>        -hilmar
>
> On Dec 7, 2005, at 6:12 PM, Angshu Kar wrote:
>
> > Hi,
> >
> > I've created 5 tables (taxon, taxon name, bioentry, biosequence,
> > biodatabase) in my postgresql database (linux box) using the biosql
> > schema
> > ddl from
> > http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/
> > biosqldb-pg.sql?rev=1.29&cvsroot=biosql&content-type=text/vnd.viewcvs-
> > markup
> >  .
> > Now I want to load the tables with arabidopsis data. Could you please
> > let me
> > know where can I find such scripts for pgsql? And also I find at
> > http://bio.perl.org/Core/Latest/index.shtml that the DB module has not
> > been
> > updated since 2001. Do I need to install that? Or are there some new
> > releases?
> >
> > I'll be obliged if you can guide.
> >
> > Thanks,
> > Angshu
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>