[Bioperl-l] A second ensembl issue rears its head . . .

[Tomso.Daniel]

Greetings.

Well, it looks like I can fetch something now, but getting anything out of it is
causing chaos.  I'm suspicious of my perl DB handling modules, as I had a bit of
trouble getting them in place.

So, I throw myself on the mercy of the list again--can someone look over the
following script and error reports?

Thanks!


#!/usr/bin/perl -w

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

my $host = 'kaka.sanger.ac.uk';
my $user = 'anonymous';
my $dbname = 'homo_sapiens_core_130';
my $remote_db = new Bio::EnsEMBL::DBSQL::DBAdaptor (-host => $host,
						  -user => $user,
						  -dbname => $dbname);

$remote_db->static_golden_path_type('NCBI_26');

my $sgp = $remote_db->get_StaticGoldenPathAdaptor;

my $vcontig = $sgp->fetch_VirtualContig_by_chr_name('2'); #OK now

my @genes = $vcontig->get_all_Genes; # this will crash

my @repeats = $vcontig->get_all_RepeatFeatures; # and so will this (comment out
the @genes bit)

# error messages attached, the 't.gene' one for the @genes version, the other
for the @repeats version

## While trying to get_all_Genes:

DBD::mysql::st execute failed: Unknown column 't.gene' in 'field list' at
/usr/lib/perl5/site_perl/5.6.0/Bio/EnsEMBL/Virtual/StaticContig.pm line 2172.
DBD::mysql::st execute failed: Unknown column 't.gene' in 'field list' at
/usr/lib/perl5/site_perl/5.6.0/Bio/EnsEMBL/Virtual/StaticContig.pm line 2172.

## While trying to get_all_RepeatFeatures:

DBD::mysql::st execute failed: Table 'homo_sapiens_core_130.analysis' doesn't
exist at /usr/lib/perl5/site_perl/5.6.0/Bio/EnsEMBL/DBSQL/Feature_Obj.pm line
474.
DBD::mysql::st execute failed: Table 'homo_sapiens_core_130.analysis' doesn't
exist at /usr/lib/perl5/site_perl/5.6.0/Bio/EnsEMBL/DBSQL/Feature_Obj.pm line
474.