[Bioperl-l] Cannot connect to local ODBA

Andy Hammer facemann at yahoo.com
Wed Jun 23 18:49:42 EDT 2004


I have altered the sample code from the ODBA HOWTO as
follows:
#!/usr/bin/perl

#use strict;
use Bio::Perl;
use Bio::DB::Registry;

$registry = Bio::DB::Registry->new;
$db = $registry->get_database('ncbi');
$seq = $db->get_Seq_by_acc('NM_000367');
print $seq->seq,"\n";

my seqdatabase.ini contains:
[ncbi]
protocol=biosql
location=localhost
dbname=biosql
driver=Pg
port=
user=     
pass=postgres
biodbname=ncbi 

But I get the error:
Can't call method "seq" on an undefined value at
./testdb.pl line 10, <FH> line 20.

I don't think it is connecting to my local db.  The
sample code that points to embl works fine.  My local
biosql database is called ncbi and it loaded fine
using load_seqdatabase.pl provided with bioperl-db. 
Any ideas?



	
		
__________________________________
Do you Yahoo!?
New and Improved Yahoo! Mail - 100MB free storage!
http://promotions.yahoo.com/new_mail 


More information about the Bioperl-l mailing list