Fixes for the alt alleles code. We needed to make sure we used the right...

Fixes for the alt alleles code. We needed to make sure we used the right variables in the code. Also needed to make sure an array is actually defined during construction

misc-scripts/alt_alleles/alt_alleles.pl

@@ -99,12 +99,12 @@ my %no_gene_id;
 my @new_groups;
 foreach my $group (@{$vega_groups}) {
   my $members = $group->get_all_Genes_types();
-  my $new_core_group = undef;
+  my $new_core_group = Bio::EnsEMBL::AltAlleleGroup->new();
   foreach my $member (@{$members}) {
     my ($vega_gene, $attribs_hash) = @{$member};
-    if(exists $vega_to_ensembl_core_gene_id{$vega_gene->stable_id()}) {
-      $new_core_group ||= Bio::EnsEMBL::AltAlleleGroup->new(); # initalise if we don't already have one
-      foreach my $gene_id (keys %{$vega_to_ens_id{$vega_stable_id}} ) {
+    my $vega_stable_id = $vega_gene->stable_id();
+    if(exists $vega_to_ensembl_core_gene_id{$vega_stable_id}) {
+      foreach my $gene_id (keys %{$vega_to_ensembl_core_gene_id{$vega_stable_id}} ) {
         #Add each gene in. If we had a 1:m relationship then we copy the attribute already assigned
         #across
         $new_core_group->add_member($gene_id, $attribs_hash);
@@ -115,7 +115,9 @@ foreach my $group (@{$vega_groups}) {
       print STDERR "no ensembl gene_id found for vega stable id $vega_stable_id in core\n";
     }
   }
-  push(@new_groups, $new_core_group);
+  if($new_core_group->size() > 0) {
+    push(@new_groups, $new_core_group);
+  }
 }
 
 #

modules/Bio/EnsEMBL/AltAlleleGroup.pm

@@ -131,7 +131,7 @@ sub new {
     my $self = $class->SUPER::new(@_);
     my ( $list ) = rearrange( [ 'MEMBERS'], @_ );
     
-    $self->{'MEMBERS'} = $list;
+    $self->{'MEMBERS'} = $list || [];
     
     return $self;
 }