using array reference rather than an array

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

@@ -9,25 +9,27 @@ 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;
+  my %biotypes;
+  foreach my $code (@attrib_codes) {
+    my ($group) = $code =~ /(\w+)\_cnt/;
+    my $biotypes = $self->get_biotype_group($group);
+    $biotypes{$code} = $biotypes;
+  }
+  return %biotypes;
+}
+
+sub get_total {
+  my ($self) = @_;
+  my $species = $self->param('species');
+  my $total = scalar(@{ Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'gene')->fetch_all });
+  return $total;
 }
 
 
 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 ($self, $slice, $key, $biotypes) = @_;
   my $count = 0;
-  foreach my $biotype (@biotypes) {
+  foreach my $biotype (@$biotypes) {
     $count += scalar(@{ $slice->get_all_Genes_by_type($biotype) });
   }
   return $count;

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

@@ -13,23 +13,27 @@ sub run {
   my $species    = $self->param('species');
   my $dba        = Bio::EnsEMBL::Registry->get_DBAdaptor($species, 'core');
 
-  my @attrib_codes = $self->get_attrib_codes();
-  $self->delete_old_attrib($dba, @attrib_codes);
+  my %attrib_codes = $self->get_attrib_codes();
+  $self->delete_old_attrib($dba, %attrib_codes);
+  my $total = $self->get_total();
+  my $sum = 0;
 
   my $slices = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'slice')->fetch_all('toplevel');
   while (my $slice = shift @$slices) {
-    foreach my $code (@attrib_codes) {
-      my $count = $self->get_feature_count($slice, $code);
-      if ($count > 0) {
-        $self->store_attrib($slice, $count, $code);
-      }
+    foreach my $code (keys %attrib_codes) {
+      my $count = $self->get_feature_count($slice, $code, $attrib_codes{$code});
+      $self->store_attrib($slice, $count, $code);
+      $sum += $count;
+    }
+    if ($sum >= $total) {
+      last;
     }
   }
 }
 
 
 sub delete_old_attrib {
-  my ($self, $dba, @attrib_codes) = @_;
+  my ($self, $dba, %attrib_codes) = @_;
   my $helper = $dba->dbc()->sql_helper();
   my $sql = q{
     DELETE sa
@@ -39,7 +43,7 @@ sub delete_old_attrib {
     AND at.attrib_type_id = sa.attrib_type_id
     AND cs.species_id = ?
     AND at.code = ? };
-  foreach my $code (@attrib_codes) {
+  foreach my $code (keys %attrib_codes) {
     $helper->execute_update(-SQL => $sql, -PARAMS => [$dba->species_id(), $code]);
   }
 }
@@ -77,6 +81,22 @@ sub store_attrib {
   $aa->store_on_Slice($slice, \@attribs);
 }
 
+sub get_biotype_group {
+  my ($self, $biotype) = @_;
+  my $prod_dba = $self->get_production_DBAdaptor();
+  my $helper = $prod_dba->dbc()->sql_helper();
+  my $sql = q{
+     SELECT name
+     FROM biotype
+     WHERE object_type = 'gene'
+     AND is_current = 1
+     AND biotype_group = ?
+     AND db_type like '%core%' };
+  my @biotypes = @{ $helper->execute_simple(-SQL => $sql, -PARAMS => [$biotype]) };
+  return \@biotypes;
+}
+
+
 
 1;