added methods to get gene counts on alternate sequences

modules/Bio/EnsEMBL/Pipeline/Production/GeneCount.pm

@@ -18,6 +18,18 @@ sub get_attrib_codes {
   return %biotypes;
 }
 
+sub get_alt_attrib_codes {
+  my ($self) = @_;
+  my @alt_attrib_codes = ('coding_acnt', 'pseudogene_acnt', 'noncoding_acnt');
+  my %biotypes;
+  foreach my $alt_code (@alt_attrib_codes) {
+    my ($group) = $alt_code =~ /(\w+)\_acnt/;
+    my $biotypes = $self->get_biotype_group($group);
+    $biotypes{$alt_code} = $biotypes;
+  }
+  return %biotypes;
+}
+
 sub get_total {
   my ($self) = @_;
   my $species = $self->param('species');
@@ -26,6 +38,26 @@ sub get_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 
+    WHERE seq_region_id NOT IN 
+    (SELECT seq_region_id 
+    FROM seq_region_attrib sa, attrib_type at
+    WHERE at.attrib_type_id = sa.attrib_type_id
+    AND at.code= "non_ref") };
+  my @ids = @{ $helper->execute_simple(-SQL => $sql) };
+  foreach my $id(@ids) {
+    push @slices, $sa->fetch_by_seq_region_id($id);
+  }
+  return \@slices;
+}
+
+sub get_all_slices {
   my ($self, $species) = @_;
   my @slices;
   my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, 'core');