[ensembl-dev] problem connecting to ensembl directly with DBConnector

Andrea Edwards edwardsa at cs.man.ac.uk
Thu Dec 30 16:50:49 GMT 2010


Hello

What should the database name be for this code to work on the ensembl 
human core/variation and cow core/variation databases?
This code works fine when it run it against local installations but says 
dbname does not exist when i run against ensembl server. I looked up 
most recent database name from ftp site.

   $dbc = Bio::EnsEMBL::DBSQL::DBConnection->new(    -user   => 
'anonymous',    -dbname => 'homo_sapiens_variation_60_37e',    -host   
=> 'ensembldb.ensembl.org',    -driver => 'mysql',  );
   # SQL statements should be created/executed through this modules
   # prepare() and do() methods.

$sql =  "select allele_id from allele limit 100";
$sth = $dbc->prepare($sql);



Could not connect to database homo_sapiens_variation_60_37e as user 
anonymous using 
[DBI:mysql:database=homo_sapiens_variation_60_37e;host=ensembldb.ensembl.org;port=3306] 
as a locator:
Unknown database 'homo_sapiens_variation_60_37e' at 
C:\Perl\site\lib\ensembl-api\ensembl\modules/Bio/EnsEMBL/DBSQL/DBConnection.pm 
line 290.

-------------------- EXCEPTION --------------------
MSG: Could not connect to database homo_sapiens_variation_60_37e as user 
anonymous using 
[DBI:mysql:database=homo_sapiens_variation_60_37e;host=ensembldb.ensembl.org;port=3306] 
as a locator:
Unknown database 'homo_sapiens_variation_60_37e'
STACK Bio::EnsEMBL::DBSQL::DBConnection::connect 
C:\Perl\site\lib\ensembl-api\ensembl\modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:299
STACK Bio::EnsEMBL::DBSQL::DBConnection::db_handle 
C:\Perl\site\lib\ensembl-api\ensembl\modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:618
STACK Bio::EnsEMBL::DBSQL::DBConnection::prepare 
C:\Perl\site\lib\ensembl-api\ensembl\modules/Bio/EnsEMBL/DBSQL/DBConnection.pm:647
STACK toplevel C:/Documents and 
Settings/Administrator/Desktop/PHD/java/Code/ensembl 
database/variation.pl:23


Are there any other ways to issue SQL queries directly?

Many thanks




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