Commit 21fb32c8 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

get_slice method specific for gene count

rather than return all toplevel slices, returns all slices with genes
does not affect much species with a reduced number of toplevel slices but increases things considerably for large number of toplevel slices
parent dc87fe33
......@@ -25,6 +25,21 @@ sub get_total {
return $total;
}
sub get_slices {
my ($self, $species) = @_;
my @slices;
my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, 'core');
my $sa = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'slice');
my $helper = $dba->dbc()->sql_helper();
my $sql = q{
SELECT DISTINCT seq_region_id FROM gene };
my @ids = @{ $helper->execute_simple(-SQL => $sql) };
foreach my $id(@ids) {
push @slices, $sa->fetch_by_seq_region_id($id);
}
return \@slices;
}
sub get_feature_count {
my ($self, $slice, $key, $biotypes) = @_;
......
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