[Bioperl-l] loading data to biosql tables

[Hilmar Lapp]

You need to install bioperl-db from CVS. There's is no good way to  
remove code that addresses those tables you don't want to instantiate,  
and frankly I don't understand why you want to spend any time on  
accommodating a truncated Biosql schema (i.e., I don't understand why  
there would be a price to instantiating the rest of the schema too).

	-hilmar


On Dec 8, 2005, at 10:09 AM, Angshu Kar wrote:

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