=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] 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
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
Questions may also be sent to the Ensembl help desk at
=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;
$Bio::EnsEMBL::CDS::VERSION = '112.0_52'; # TRIAL
$Bio::EnsEMBL::CDS::VERSION = '112.052';
use vars qw(@ISA);
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;