[Bioperl-l] Can someone take a look at this ensembl script?

[Tomso.Daniel]

Greetings.

I think I've got the relevant support and db modules, etc, installed for using
the ensembl modules.  However, some scripts seem to work and some don't, which
is vexing.

Can somebody take a look at the following/run it to see whether there is a
problem with my configuration?

This is basically right out of the EnsEMBL tutorial document (or nearly so).

Along these lines, it seems like a number of things associated w/ the ensembl
code are problematic.  Is there a good way to get into this aside from the
tutorial document at www.ensembl.org?

DT


#!/usr/bin/perl -w

use Bio::EnsEMBL::DBSQL::DBAdaptor;

# Note: this throws an exception for both a local ensembl server and kaka.sanger
# Msg: Cannot build virtual contig from no raw contigs.  Probably an error in
the call to get raw contigs

my $host = 'kaka.sanger.ac.uk';
my $user = 'anonymous';
my $dbname = 'homo_sapiens_core_130';
my $core_db = new Bio::EnsEMBL::DBSQL::DBAdaptor (-host => $host,
						  -user => $user,
						  -dbname => $dbname);
$core_db->static_golden_path_type('NCBI_26');
my $sgp = $core_db->get_StaticGoldenPathAdaptor;
my $vcontig = $sgp->fetch_VirtualContig_by_chr_name('chr2');