diff --git a/modules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm b/modules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm index 83a5bf86205c65da98d8544723ed2451c754237f..944e5cf163ac46855e4da52cf5f8d3ca71b2c071 100644 --- a/modules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm +++ b/modules/Bio/EnsEMBL/Pipeline/Production/PepStats.pm @@ -13,6 +13,10 @@ sub run { my $species = $self->param('species'); my $dbtype = $self->param('dbtype'); my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $dbtype); + if ( $dbtype =~ 'vega' || $dbtype =~ 'otherf' ) { + my $core_dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, 'core'); + $dba->dnadb($core_dba); + } my $helper = $dba->dbc()->sql_helper(); my %attrib_codes = $self->get_attrib_codes(); @@ -116,7 +120,8 @@ sub get_attrib_codes { sub dump_translation { my ($self, $dba, $tmpfile) = @_; my $helper = $dba->dbc()->sql_helper(); - my $ta = Bio::EnsEMBL::Registry->get_adaptor($self->param('species'), 'core', 'translation'); + my $dbtype = $self->param('dbtype'); + my $ta = Bio::EnsEMBL::Registry->get_adaptor($self->param('species'), $dbtype, 'translation'); open(TMP, "> $tmpfile"); my $sql = q{ SELECT tl.translation_id