check length when retrieving exon peptide - some transcripts have incomplete last codons

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -25,8 +25,6 @@ accepts them (at the moment) in a transcript.
   Elia Stupka  : elia@ebi.ac.uk
   Ewan Birney  : 
 
-=head1 APPENDIX
-
 =cut
 
 package Bio::EnsEMBL::DBSQL::TranscriptAdaptor;
@@ -164,7 +162,6 @@ sub fetch_by_translation_stable_id {
  Returns : 
  Args    : needs a gene ...
 
-
 =cut
 
 sub store {

modules/Bio/EnsEMBL/Exon.pm

@@ -1100,7 +1100,14 @@ sub peptide {
 		 " Is this exon [$self] a member of this transcript [$tr]?");
   } elsif(scalar(@coords) == 1) {
     my $c = $coords[0];
-    $pep_str = $tr->translate->subseq($c->start, $c->end);
+    my $pep = $tr->translate;
+
+    #bioperl doesn't give back residues for incomplete codons
+    #make sure we don't subseq too far...
+    my ($start, $end);
+    $end = ($c->end > $pep->length) ? $pep->length : $c->end; 
+    $start = ($c->start < $end) ? $c->start : $end;
+    $pep_str = $tr->translate->subseq($start, $end);
   }
     
   return Bio::Seq->new(-seq => $pep_str,