ENSCORESW-1663: get_all_CDS_introns method

modules/Bio/EnsEMBL/Transcript.pm

@@ -1644,6 +1644,37 @@ sub get_all_Introns {
    return \@introns;
 }
 
+=head2 get_all_CDS_Introns
+
+  Arg [1]    : none
+  Example    : my @introns = @{$transcript->get_all_CDS_Introns()};
+  Description: Returns an listref of the introns between coding exons in this transcript in order.
+  Returntype : listref to Bio::EnsEMBL::Intron objects
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub get_all_CDS_Introns {
+   my ($self) = @_;
+   # return an empty list if there is no translation
+   my $translation = $self->translation or return [];
+   if( ! defined $self->{'_trans_exon_array'} && defined $self->adaptor() ) {
+     $self->{'_trans_exon_array'} = $self->adaptor()->db()->
+       get_ExonAdaptor()->fetch_all_by_Transcript( $self );
+   }
+
+   my @introns=();
+   my @exons = @{$self->{'_trans_exon_array'}};
+   for(my $i=0; $i < scalar(@exons)-1; $i++){
+     if (!$exons[$i]->is_coding($self)) { next; }
+     my $intron = new Bio::EnsEMBL::Intron($exons[$i],$exons[$i+1]);
+     push(@introns, $intron)
+   }
+   return \@introns;
+}
+
 
 =head2 length
 

modules/t/transcript.t

@@ -351,11 +351,19 @@ foreach my $stable_id (qw(ENST00000201961 ENST00000217347)){ #test both strands
   my @exons = (@{$transcript->get_all_Exons()});
   my @introns = (@{$transcript->get_all_Introns()});
 
+  my @cds = (@{$transcript->get_all_CDS()});
+  my @cds_introns = (@{$transcript->get_all_CDS_Introns()});
+
   my $orig_seq = $transcript->slice->subseq(
 					    $transcript->start(),
 					    $transcript->end(), 
 					    $transcript->strand());
 
+  my $cds_orig_seq = $transcript->slice->subseq(
+                                            $transcript->coding_region_start(),
+                                            $transcript->coding_region_end(),
+                                            $transcript->strand());
+
   my $idl=0;
   my $new_seq = $exons[0]->seq()->seq();
   foreach my $intron (@introns){
@@ -367,6 +375,17 @@ foreach my $stable_id (qw(ENST00000201961 ENST00000217347)){ #test both strands
 
   is($orig_seq, $new_seq, 'Correct new origin seq');
 
+  my $cds_idl=0;
+  my $new_cds_seq = $cds[0]->seq();
+  foreach my $cds_intron (@cds_introns){
+    $new_cds_seq .= $cds_intron->seq;
+    $new_cds_seq .= $cds[$cds_idl+1]->seq();
+    $cds_idl++;
+
+  }
+
+  is($cds_orig_seq, $new_cds_seq, 'Correct new cds origin seq');
+
 }