[Bioperl-l] loading data to biosql tables

[Angshu Kar]

Thank you Hilmar. Actually we want only those tables for our tests!
Also at first, do I need to install the Bioperl-db module ( But is it the
one that was updated 4 years back or are there any new releases)? And then
run the script suggested by you in the box? Can't we just edit the script
and keep those parts that correspond to only the tables that I've created?

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
> -------------------------------------------------------------
>
>
>