new gene count method, divided in coding/pseudogene/noncoding groups

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

+package Bio::EnsEMBL::Pipeline::Production::GeneCount;
+
+use strict;
+use warnings;
+
+use base qw/Bio::EnsEMBL::Pipeline::Production::StatsGenerator/;
+
+
+sub get_attrib_codes {
+  my ($self) = @_;
+  my @attrib_codes = ('coding_cnt', 'pseudogene_cnt', 'noncoding_cnt');
+  return @attrib_codes;
+}
+
+
+sub get_feature_count {
+  my ($self, $slice, $key) = @_;
+  my $prod_dba    = $self->get_production_DBAdaptor();
+  my $prod_helper = $prod_dba->dbc()->sql_helper();
+  my ($group) = $key =~ /(\w+)\_cnt/;
+  my $sql = q{
+    SELECT name
+    FROM biotype
+    WHERE biotype_group = ?
+    AND object_type = 'gene'
+    AND is_current = 1
+    AND db_type like '%core%' };
+  my @biotypes = @{ $prod_helper->execute_simple(-SQL => $sql, -PARAMS => [$group]) };
+  my $count = 0;
+  foreach my $biotype (@biotypes) {
+    $count += scalar(@{ $slice->get_all_Genes_by_type($biotype) });
+  }
+  return $count;
+}
+
+
+1;
+