use display_id instead of primary id for xrefs

added mRNA to feature table
CDS is now actually CDS when there is UTR
pseudogenes dump as misc_RNA instead of as CDS

modules/Bio/EnsEMBL/Utils/SeqDumper.pm

@@ -620,22 +620,41 @@ sub _dump_feature_table {
     foreach my $gene (@{$gene_slice->get_all_Genes}) {
       foreach my $transcript (@{$gene->get_all_Transcripts}) {
 	my $translation = $transcript->translation;
-	$value = $self->features2location($transcript->get_all_Exons);
-	$self->write(@ff,'CDS', $value);
-	$self->write(@ff,''   , '/gene="'.$gene->stable_id().'"');
-	$translation && 
-	  $self->write(@ff,'', '/protein_id="'.$translation->stable_id().'"');
-	$self->write(@ff,''
-		     ,'/note="transcript_id='.$transcript->stable_id().'"');
-
-	foreach my $dbl (@{$transcript->get_all_DBLinks}) {
-	  $value = '/db_xref="'.$dbl->dbname().':'.$dbl->primary_id().'"';
-	  $self->write(@ff, '', $value);
-	}
-	if($translation) { 
+        
+        # normal transcripts get dumped differently than pseudogenes
+        if($translation) {
+          #normal transcript
+          $value = $self->features2location($transcript->get_all_Exons);
+          $self->write(@ff, 'mRNA', $value);
+          $self->write(@ff,''   , '/gene="'.$gene->stable_id().'"');
+
+          # ...and a CDS section
+          $value = 
+            $self->features2location($transcript->get_all_translateable_Exons);
+          $self->write(@ff,'CDS', $value);
+          $self->write(@ff,''   , '/gene="'.$gene->stable_id().'"'); 
+          $self->write(@ff,'', '/protein_id="'.$translation->stable_id().'"');
+          $self->write(@ff,''
+                       ,'/note="transcript_id='.$transcript->stable_id().'"');
+          
+          foreach my $dbl (@{$transcript->get_all_DBLinks}) {
+            $value = '/db_xref="'.$dbl->dbname().':'.$dbl->display_id().'"';
+            $self->write(@ff, '', $value);
+          }
+
 	  $value = '/translation="'.$transcript->translate()->seq().'"';
 	  $self->write(@ff, '', $value);
-	}
+        } else {
+          #pseudogene
+          $value = $self->features2location($transcript->get_all_Exons);
+          $self->write(@ff, 'misc_RNA', $value);
+          $self->write(@ff,''   , '/gene="'.$gene->stable_id().'"');
+          foreach my $dbl (@{$transcript->get_all_DBLinks}) {
+            $value = '/db_xref="'.$dbl->dbname().':'.$dbl->primary_id().'"';
+            $self->write(@ff, '', $value);
+          }
+          $self->write(@ff,''   , '/note="pseudogene"');
+        }
       }
     }
       
@@ -660,7 +679,7 @@ sub _dump_feature_table {
       $self->write(@ff, 'mRNA', $self->features2location($exons));
       $self->write(@ff, '', '/product="'.$transcript->translate()->seq().'"');
       $self->write(@ff, '', '/note="Derived by automated computational' .
-		   'analysis using gene prediction method:' . 
+		   ' analysis using gene prediction method:' . 
 		   $transcript->analysis->logic_name . '"');
     }
   }