StopCodonReadthroughEdit.pm

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=head1 LICENSE
 
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Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
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     http://www.apache.org/licenses/LICENSE-2.0
 
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=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 RefSeq 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_rt');
 
  return $stop_codon_rt_edit;
 
}
 
1;