[Bioperl-l] Re: Bio::DB::Query

Hilmar Lapp hlapp at gmx.net
Wed Apr 20 14:01:50 EDT 2005


the Bio::DB::Query is bioperl-db, not biojava or java for that matter, 
so if this is what you're trying to use then email to the bioperl 
(bioperl-l at bioperl.org) list, or for schema-related and SQL questions 
the biosql (biosql-l at open-bio.org) list.

Bio::DB::Query::BioQuery will map classes to tables for you. There's no 
really good HowTo document yet; there's plenty of examples though in 
the respective test script t/query.t.

I don't understand your goal in modifying load_seqdatabase.pl, so 
unless you elaborate on what you're trying to achieve I can't help you.

As for SQL queries and your example, you don't need bioperl-db to issue 
SQL queries against biosql - just use your favorite SQL shell for your 
RDBMS of choice (mysql for MySQL, psql for PostgreSQL, etc) and type in 
queries there. Bioperl-db is not meant to replace or provide a SQL 
shell functionality.

If this doesn't help you will need to be more specific on what you're 
trying to achieve.


On Tuesday, April 19, 2005, at 03:15  PM, carito vargas wrote:

> Hello,
> I am trying to modify the script load_seqdatabase.pl and I wanted to
> do a "select MAX(identifier) from bioentry", kind of simple but  and I
> found it very complicated using Bio::DB::Query
> I read the documentation, but I don't understand how to construct the
> query... we have to give clases arguments mapped to tables??
> Please, if anyone can give me a clear example I would be thankfull
> Carito Vargas
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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