[Bioperl-l] Help using bioperl-db

[Ewan Birney]

On Fri, 9 Nov 2001, gert thijs wrote:

> Hello,
> 
> I just installed bioperl-db and created a mysql database, called 'SeqDB', to
> store my DNA sequences and later extract them. 
> Next, I have created the tables as explained in the README file: 
>  mysql -h bowmore -u thijs -p SeqDB < sql/basicseqdb-mysql.sql
> This works fine and all tables are created.

great!

> 
> Now, I am looking at the program 'script/load_seqdatabase.pl' to store a set
> of sequences in GenBank format into the database. But I have some trouble
> understanding the usage of a few variables. So I have some questions. First,
> what is the purpose of $sqlname and $dbname and what is the difference between
> them? Second, this is related to the first one: what is t he purpose of 
> $dbid =
> $dbadaptor->get_BioDatabaseAdaptor->fetch_by_name_store_if_needed($dbname);
> 


sqlname is the (mysql) database name for the whole collection of databases


Inside the *same* mysql database name you can store *mutliple* biological
"databases" (such as GenBank or Swissprot or Whatever). Of course you
could provide the rule that sqlname == dbname for your set, but it is easy
to imagine people who want to put multiple biological databases into one
sql database 


hence the difference.




> can anyone help me here.
> 
> Thanks,
> Gert Thijs
> 
> 
> 
> -- 
> + Gert Thijs              
> + 
> + email: gert.thijs@esat.kuleuven.ac.be 
> + homepage: http://www.esat.kuleuven.ac.be/~thijs
> + 
> + K.U.Leuven
> + ESAT-SISTA 
> + Kasteelpark Arenberg 10 
> + B-3001 Leuven-Heverlee  
> + Belgium  
> + Tel : +32 16 32 85 88 (new number)
> + Fax : +32 16 32 19 70
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------