added methods to get count on alternate sequences

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

@@ -15,24 +15,57 @@ sub run {
 
   my %attrib_codes = $self->get_attrib_codes();
   $self->delete_old_attrib($dba, %attrib_codes);
+  my %alt_attrib_codes = $self->get_alt_attrib_codes();
+  $self->delete_old_attrib($dba, %alt_attrib_codes);
   my $total = $self->get_total();
   my $sum = 0;
+  my $count;
+  my %slices_hash;
 
   my $slices = $self->get_slices($species);
-  my @sorted_slices = 
+  my $all_slices = $self->get_all_slices($species);
+  foreach my $region (@$slices) {
+    $slices_hash{$region->name} = 1;
+  }
+
+print scalar(@$slices) . " ref slices and " . scalar(@$all_slices) . " all slices\n" ;
+  if (scalar(@$slices) == scalar(@$all_slices)) {
+    my @sorted_slices = 
      sort( { $a->coord_system()->rank() <=> $b->coord_system()->rank()
              || $b->seq_region_length() <=> $a->seq_region_length() } @$slices) ;
 
-  while (my $slice = shift @sorted_slices) {
-    foreach my $code (keys %attrib_codes) {
-      my $count = $self->get_feature_count($slice, $code, $attrib_codes{$code});
-      if ($count > 0) {
-        $self->store_attrib($slice, $count, $code);
+    while (my $ref_slice = shift @sorted_slices) {
+      foreach my $code (keys %attrib_codes) {
+        $count = $self->get_feature_count($ref_slice, $code, $attrib_codes{$code});
+        if ($count > 0) {
+          $self->store_attrib($ref_slice, $count, $code);
+        }
+        $sum += $count;
+      }
+      if ($sum >= $total) {
+        last;
       }
-      $sum += $count;
     }
-    if ($sum >= $total) {
-      last;
+  } else {
+    my @all_sorted_slices =
+     sort( { $a->coord_system()->rank() <=> $b->coord_system()->rank()
+             || $b->seq_region_length() <=> $a->seq_region_length() } @$all_slices) ;
+    while (my $slice = shift @all_sorted_slices) {
+      if (exists $slices_hash{$slice->name}) {
+        foreach my $ref_code (keys %attrib_codes) {
+          $count = $self->get_feature_count($slice, $ref_code, $attrib_codes{$ref_code});
+          if ($count > 0) {
+            $self->store_attrib($slice, $count, $ref_code);
+          }
+        }
+      } else {
+        foreach my $alt_code (keys %alt_attrib_codes) {
+          my $alt_count = $self->get_feature_count($slice, $alt_code, $alt_attrib_codes{$alt_code});
+          if ($alt_count > 0) {
+            $self->store_attrib($slice, $alt_count, $alt_code);
+          }
+        }
+      }
     }
   }
 }
@@ -43,6 +76,11 @@ sub get_slices {
   return $slices;
 }
 
+sub get_all_slices {
+  my ($self, $species) = @_;
+  my $slices = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'slice')->fetch_all('toplevel', undef, 1);
+  return $slices;
+}
 
 sub delete_old_attrib {
   my ($self, $dba, %attrib_codes) = @_;