Merge pull request #372 from Ensembl/feature/stop_codon_readthrough_edit

Add support for stop codon readthrough as a type of edit. 

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
+
+  use Bio::EnsEMBL::StopCodonReadthroughEdit;
+
+  # Get transcript
+  my $transcript_adaptor = $db->get_TranscriptAdaptor();
+  my $transcript = $transcript_adaptor->fetch_by_stable_id("ENST00000217347");
+  $transcript->edits_enabled(1);
+  print "Before modifiction: $transcript->translate->seq()\n";
+
+  # Construct a stop codon readthrough edit object
+  my $stop_codon_readthrough_edit = Bio::EnsEMBL::StopCodonReadthroughEdit->new(265);
+
+  # Apply post translation edit
+  $transcript->translation->add_Attributes($stop_codon_readthrough_edit->get_Attribute());
+  my $translated_sequence = $transcript->translate->seq();
+  print "After modifiction: $translated_sequence\n";
+
+=head1 DESCRIPTION
+
+  Biologically, STOP codon readthrough is a rare phenomenon whereby translation
+  does not terminate at an in-frame STOP codon, but instead continues further downstream.
+  It is believed the STOP codon is instead read as a 'sense' codon, i.e. encodes for an amino acid.
+
+  The location of a STOP codon readthrough is indicated by an asterisk (*) in the post translation sequence.
+  This class edits the sequence to replace the asterisk (*) with an 'X' to make it similar to Uniprot representation.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::StopCodonReadthroughEdit;
+
+use strict;
+use warnings;
+
+use parent qw(Bio::EnsEMBL::SeqEdit);
+
+=head2 new
+
+  Arg [-POSITION]  :
+       int - start and end position of the stop codon readthrough edit in the sequence
+
+  Example    : $stop_codon_rt_edit = Bio::EnsEMBL::StopCodonReadthroughEdit->new($position);
+  Description: Creates a new stop codon readthrough edit object
+  Returntype : Bio::EnsEMBL::StopCodonReadthroughEdit
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub new {
+  my ($self, $position) = @_;
+
+  my $class = ref($self) || $self;
+  my $stop_codon_rt_edit = $class->SUPER::new(
+        -START   => $position,
+        -END     => $position,
+        -ALT_SEQ => 'X',
+        -CODE    => '_stop_codon_readthrough');
+
+  return $stop_codon_rt_edit;
+
+}
+
+1;

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/test-genome-DBs/homo_sapiens/core/attrib_type.txt

@@ -20,3 +20,4 @@
 20	proj_parent_g	projection parent gene	Stable identifier of the parent gene this gene was projected from (projection between different species and/or assemblies).
 21	proj_parent_t	projection parent transcript	Stable identifier of the parent transcript this transcript was projected from (projection between different species and/or assemblies).
 22	mirna_arm	miRNA arm	Hairpin arm from which this miRNA has come from
+23	_stop_codon_readthrough	Stop Codon Readthrough	\N

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;
@@ -343,4 +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");
 
+#56-57
+#
+# Handling stop codon readthrough edit
+#
+
+my $transcript_adaptor = $db->get_TranscriptAdaptor();
+$transcript = $transcript_adaptor->fetch_by_stable_id("ENST00000217347");
+$transcript->edits_enabled(1);
+
+diag 'Before X insertion: ', explain($transcript->translate->seq());
+
+my $stop_codon_rt_edit = Bio::EnsEMBL::StopCodonReadthroughEdit->new(265);
+$transcript->translation->add_Attributes($stop_codon_rt_edit->get_Attribute());
+my $translated_sequence = $transcript->translate->seq();
+
+diag 'After X insertion: ', explain($translated_sequence);
+is($translated_sequence =~ /QEEXEE/, 1, 'X inserted');
+is(length($transcript->translate->seq()), length($translated_sequence), 'Length of the sequence pre and post edit is equal');
+
 done_testing();