[Bioperl-l] loading data to biosql tables

[Hilmar Lapp]

Angshu, load_seqdatabase.pl is a script that utilizes the language  
binding library bioperl-db to load sequences and annotation into  
Biosql. The object-relational mapping code is all over bioperl-db.

I'm sorry, but if you believe it is worth fiddling with that  
object-relational code to 'save' instantiating a few more tables then  
you're welcome to do so but you're essentially on your own.

Also, if you'd like to work with a schema the language binding of which  
allows to arbitrarily drop tables from the schema and still work then  
Biosql/bioperl-db may not be for you.

	-hilmar

On Dec 9, 2005, at 7:10 AM, Angshu Kar wrote:

> 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
>> -------------------------------------------------------------
>>
>>
>>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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