CDS.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
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::CDS - Object representing a CDS
 
=head1 SYNOPSIS
 
  use Bio::EnsEMBL::CDS;
 
  $feature = Bio::EnsEMBL::CDS->new(
    -start         => 100,
    -end           => 220,
    -strand        => -1,
    -slice         => $slice,
    -phase         => 1,
    -transcript    => $transcript
  );
 
=head1 DESCRIPTION
 
This is a CDS feature within the Ensembl CDS.
It represents the coding regions of a transcript.
 
=head1 METHODS
 
=cut
 
use strict;
 
package Bio::EnsEMBL::CDS;
 
use vars qw(@ISA);
 
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Scalar::Util qw(weaken isweak);
 
@ISA = qw(Bio::EnsEMBL::Feature);
 
use constant SEQUENCE_ONTOLOGY => {
  acc  => 'SO:0000316',
  term => 'CDS',
};
 
=head2 new
 
  Arg [...]  : Named arguments passed to superclass
  Example    : $feature = Bio::EnsEMBL::CDS->new
                        (-start   => 1,
                         -end     => 100,
                         -strand  => 1,
                         -slice   => $slice,
                         -dbID    => 10,
                         -transcript  => $transcript,
                         -phase   => 1);
  Description: Constructs a new Bio::EnsEMBL::CDS.
  Returntype : Bio::EnsEMBL::CDS
  Exceptions : Thrown on invalid -SLICE, -STRAND arguments
  Caller     : general, subclass constructors
  Status     : Stable
 
=cut
 
sub new {
  my $caller = shift;
 
  #allow this to be called as class or object method
  my $class = ref($caller) || $caller;
  my $self = $class->SUPER::new(@_);
 
  my ($transcript, $phase, $translation_id, $seq_region_start, $seq_region_end) = rearrange(['TRANSCRIPT','PHASE', 'TRANSLATION_ID', 'SEQ_REGION_START', 'SEQ_REGION_END'],@_);
 
  $self->{'transcript'} = $transcript;
  $self->{'phase'} = $phase;
  $self->{'translation_id'} = $translation_id;
  $self->{'seq_region_start'} = $seq_region_start;
  $self->{'seq_region_end'} = $seq_region_end;
 
  return $self;
}
 
 
=head2 transcript
 
  Arg [1]    : (optional) Bio::EnsEMBL::Transcript
  Example    : $transcript = $cds->transcript();
  Description: Getter/Setter for the transcript associated with this
               CDS.
  Returntype : Bio::EnsEMBL::Transcript
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub transcript {
  my $self = shift;
  $self->{'transcript'} = shift if(@_);
  return $self->{'transcript'};
}
 
=head2 translation
 
    Description: Fetch the translation associated with
                 this transcript, if it exists. Return undef
                 if there is no translation, ie. a pseudogene
    Returntype : Bio::EnsEMBL::Translation or undef
    Caller     : general
    Status     : Stable
 
=cut
 
sub translation {
    my $self = shift;
    return $self->transcript()->translation();
}
 
=head2 seq_region_start
 
  Arg [1]    : (optional) string $seq_region_start
  Example    : $seq_region_start = $cds->seq_region_start();
  Description: Getter/Setter for the seq_region_start for this CDS.
               Overwrite default method from Feature as CDS does not have
               a table
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub seq_region_start {
  my $self = shift;
  $self->{'seq_region_start'} = shift if(@_);
  return $self->{'seq_region_start'};
}
 
=head2 seq_region_end
 
  Arg [1]    : (optional) string $seq_region_end
  Example    : $seq_region_end = $cds->seq_region_end();
  Description: Getter/Setter for the seq_region_end for this CDS.
               Overwrite default method from Feature as CDS does not have
               a table
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub seq_region_end {
  my $self = shift;
  $self->{'seq_region_end'} = shift if(@_);
  return $self->{'seq_region_end'};
}
 
=head2 get_Gene
 
  Description: Get the gene associated with the ExonTranscript,
               if a transcript has been set
  Returntype : Bio::EnsEMBL::Gene or undef
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub get_Gene {
    my $self = shift;
 
    if($self->{'transcript'}) {
    return $self->{'transcript'}->get_Gene();
    }
 
    return;
}
 
=head2 translation_id
 
  Arg [1]    : (optional) string $translation_id
  Example    : $translation_id = $cds->translation_id();
  Description: Getter/Setter for the stable_id for the translation
               associated with this CDS.
  Returntype : String
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub translation_id {
  my $self = shift;
  $self->{'translation_id'} = shift if(@_);
  return $self->{'translation_id'};
}
 
 
=head2 phase
 
  Arg [1]    : (optional) string $phase
  Example    : print $cds->phase();
  Description: This method returns an integer that describes
               the phase of the coding feature
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub phase {
  my $self = shift;
  $self->{'phase'} = shift if( @_ );
  return ( $self->{'phase'} || 0 );
}
 
 
=head2 summary_as_hash
 
  Example    : my $hash = $cds->summary_as_hash();
  Description: Generates a HashRef compatible with GFFSerializer. Adds
               Parent, source and phase to the basic feature hash
  Returntype : Hash
  Exceptions : none
  Caller     : general
  Status     : Stable
 
=cut
 
sub summary_as_hash {
  my ($self) = @_;
  my $hash = $self->SUPER::summary_as_hash();
  $hash->{'phase'} = $self->phase();
  my $parent = $self->transcript();
  $hash->{'Parent'} = $parent->display_id if defined $parent;
  $hash->{'source'} = $self->transcript->source() if $self->transcript();
  $hash->{'id'} = $self->translation_id() if $self->translation_id();
  $hash->{'protein_id'} = $self->translation_id() if $self->translation_id();
  return $hash;
}
 
 
1;