Code updated to implement review comments. There is a new package to handle...

Code updated to implement review comments. There is a new package to handle stop codon readthrough in a sequence. Test case has been updated with new regex

modules/Bio/EnsEMBL/StopCodonReadthroughEdit.pm

+=head1 LICENSE
+
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+Copyright [2016-2019] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <http://www.ensembl.org/Help/Contact>.
+
+=cut
+
+=head1 NAME
+
+  Bio::EnsEMBL::StopCodonReadthroughEdit - Object representing a stop codon readthrough edit in a sequence
+
+=head1 SYNOPSIS
+
+  my $stopcodonrtedit = Bio::EnsEMBL::StopCodonReadthroughEdit->new($coord);
+
+=head1 DESCRIPTION
+
+  A representation of a stop codon readthrough edit in a sequence. 
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::StopCodonReadthroughEdit;
+
+use strict;
+
+use parent qw(Bio::EnsEMBL::SeqEdit);
+
+=head2 new
+
+  Arg [-START/END]  : 
+       int - start and end postion of the stop codon readthrough edit in the sequence
+  
+  Example    : $stopcodonrtedit = Bio::EnsEMBL::StopCodonReadthroughEdit->new($coord);
+  Description: Creates a new stop codon readthrough edit object
+  Returntype : Bio::EnsEMBL::StopCodonReadthroughEdit
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub new {
+  my ($self, $coord) = @_;
+  my $caller = shift;
+   
+  my $class = ref($caller) || $caller;
+  my $self = $class->SUPER::new(        
+        -START   => $coord,
+        -END     => $coord,
+        -ALT_SEQ => 'X',
+        -CODE    => '_stop_codon_readthrough',
+        -NAME    => 'Stop Codon Readthrough');
+
+  return $self;
+
+}
+
+1;

modules/t/translation.t

@@ -19,6 +19,7 @@ use warnings;
 use Bio::EnsEMBL::Test::TestUtils;
 use Bio::EnsEMBL::Translation;
 use Bio::EnsEMBL::Exon;
+use Bio::EnsEMBL::StopCodonReadthroughEdit;
 
 use Test::More;
 use Test::Warnings;
@@ -343,28 +344,23 @@ 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
-##
+#56-57
+#
+# Handling stop codon readthrough edit
+#
 
 my $tra_scrt = $db->get_TranscriptAdaptor();
 my $tr_scrt = $tra_scrt->fetch_by_stable_id("ENST00000217347");
-
 $tr_scrt->edits_enabled(1);
 
-my $scrt = Bio::EnsEMBL::SeqEdit->new(
-  -START   => 1,
-  -END     => 2,
-  -ALT_SEQ => 'X',
-  -CODE    => '_stop_codon_readthrough',
-  -NAME    => 'Stop Codon Readthrough'
-);
+diag 'Before X insertion: ', explain($tr_scrt->translate->seq());
 
+my $scrt = Bio::EnsEMBL::StopCodonReadthroughEdit->new(265);
 $tr_scrt->translation->add_Attributes($scrt->get_Attribute());
-
 my $tlseq_scrt = $tr_scrt->translate->seq();
-debug("X inserted: " . $tlseq_scrt);
-is($tlseq_scrt =~ /X/, 1, 'X inserted');
+
+diag 'After X insertion: ', explain($tlseq_scrt);
+is($tlseq_scrt =~ /QEEXEE/, 1, 'X inserted');
+is(length($tr_scrt->translate->seq()), length($tlseq_scrt), 'Length of the sequence pre and post edit is equal');
 
 done_testing();