ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The...

ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The code edits the amino acid sequence to display the stop codon readthrough with an X

modules/Bio/EnsEMBL/Translation.pm

@@ -1108,7 +1108,7 @@ sub get_all_SeqEdits {
 
   my $attribs;
   
-  $edits ||= ['initial_met', '_selenocysteine', 'amino_acid_sub'];
+  $edits ||= ['initial_met', '_selenocysteine', 'amino_acid_sub', '_stop_codon_readthrough'];
   
 
   foreach my $edit(@{wrap_array($edits)}){
@@ -1137,6 +1137,20 @@ sub get_all_selenocysteine_SeqEdits {
   return $self->get_all_SeqEdits(['_selenocysteine']);
 }
   
+=head2 get_all_stop_codon_SeqEdits
+
+  Example    : my @edits = @{$translation->get_all_stop_codon_SeqEdits()};
+  Description: Retrieves all post transcriptional sequence modifications related
+               to stop codon readthrough
+  Returntype : Bio::EnsEMBL::SeqEdit
+  Exceptions : none
+
+=cut
+
+sub get_all_stop_codon_SeqEdits {
+  my ($self) = @_;
+  return $self->get_all_SeqEdits(['_stop_codon_readthrough']);
+}
 
 =head2 modify_translation
 

modules/t/translation.t

@@ -343,4 +343,28 @@ ok(!scalar(@alt_tls));
 # Test generic_count(), inherited method from BaseAdaptor
 is($ta->generic_count(), @{$ta->list_dbIDs()}, "Number of features from generic_count is equal to the number of dbIDs from list_dbIDs");
 
+#56
+##
+## Handling stop codon readthrough
+##
+
+my $tra_scrt = $db->get_TranscriptAdaptor();
+my $tr_scrt = $tra_scrt->fetch_by_stable_id("ENST00000217347");
+
+$tr_scrt->edits_enabled(1);
+
+my $scrt = Bio::EnsEMBL::SeqEdit->new(
+  -START   => 1,
+  -END     => 2,
+  -ALT_SEQ => 'X',
+  -CODE    => '_stop_codon_readthrough',
+  -NAME    => 'Stop Codon Readthrough'
+);
+
+$tr_scrt->translation->add_Attributes($scrt->get_Attribute());
+
+my $tlseq_scrt = $tr_scrt->translate->seq();
+debug("X inserted: " . $tlseq_scrt);
+is($tlseq_scrt =~ /X/, 1, 'X inserted');
+
 done_testing();