EMBL dumping changes - not tested

modules/Bio/EnsEMBL/Utils/EMBL/SliceWrapper.pm

@@ -234,7 +234,7 @@ sub ac {
 sub id {
   my $self = shift;
 
-  return $self->ac;
+  return $self->slice->name;
 }
 
 
@@ -389,24 +389,23 @@ sub top_SeqFeatures {
   #filter out features overlapping slice boundary
   my @out = ();
   my $slice_end   = $self->slice->chr_end;
-  foreach my $f (@sfs) {
-    next if($f->start < 1 || $f->end > $slice_end);
-    push @out, $f;
+  while($f = shift @sfs) {
+    push(@out, $f) unless($f->start < 1 || $f->end > $slice_end);    
   }
 
   #transcripts and genes are allowed to overlap boundary
   unless($self->skip_SeqFeature('prediction')) {
     foreach my $pt (@{$self->slice->get_all_PredictionTranscripts}) {
-      push @sfs, new Bio::EnsEMBL::Utils::EMBL::TranscriptWrapper($pt);
+      push @out, new Bio::EnsEMBL::Utils::EMBL::TranscriptWrapper($pt);
     }
   }
   unless($self->skip_SeqFeature('gene')) {
     foreach my $gene (@{$self->slice->get_all_Genes()}) {
-      push @sfs, new Bio::EnsEMBL::Utils::EMBL::GeneWrapper($gene);
+      push @out, new Bio::EnsEMBL::Utils::EMBL::GeneWrapper($gene);
     }
   }
-  
-  return @sfs;
+
+  return @out;
 }
 
 

modules/Bio/EnsEMBL/Utils/EMBL/TranscriptWrapper.pm

@@ -137,7 +137,15 @@ sub to_FTHelper {
 
   my $ft = Bio::SeqIO::FTHelper->new();
   $ft->loc($loc);
-  $ft->key('CDS');
+
+  my $exon_key;
+  if($trans->isa('Bio::EnsEMBL::PredictionTranscript')) {
+      $ft->key('CDS');
+      $exon_key = 'exon';
+  } else {
+      $ft->key('CDS_' . $trans->analysis->logic_name);
+      $exon_key = 'exon_' . $trans->analysis->logic_name;
+  }
   
   $ft->add_field('translation', $trans->translate()->seq());
   if($trans->can('translation')) {
@@ -148,12 +156,12 @@ sub to_FTHelper {
     $ft->add_field('db_xref', $dbl->database().":".$dbl->primary_id());
   }
   push(@out, $ft);
-  
+
   foreach my $exon (@{$trans->get_all_translateable_Exons()}) {
     my $ft = Bio::SeqIO::FTHelper->new();
 
     $ft->loc(features2join_string([$exon]));
-    $ft->key("exon");
+    $ft->key($exon_key);
     
     if( $self->strict_EMBL_dumping()) {
       $ft->add_field('db_xref', 'ENSEMBL:HUMAN-Exon-'.$exon->stable_id());