Raw content of Bio::EnsEMBL::Variation::ConsequenceType
<![CDATA[# EnsEMBL module for ConsequenceType
# Copyright EMBL-EBI/Sanger center 2005
#
#
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Variation::ConsequenceType
=head1 SYNOPSIS
=head1 DESCRIPTION
Represents the effect of a Variation in a Transcript
=cut
package Bio::EnsEMBL::Variation::ConsequenceType;
use strict;
use Bio::EnsEMBL::Utils::Exception qw(warning);
#conversion of consequence type to bit value
#there is a special type, SARA, that only applies to the effect of the Alleles, not Variations, and is equivalent
#to Same As Reference Allele, meaning that the Allele is the same as in reference sequence, so has no effect
#but it is not stored anywhere in the database and need no conversion at all
#when creating the VariationFeature object, thus the absence in the hash
our %CONSEQUENCE_TYPES = ('ESSENTIAL_SPLICE_SITE' => 1,
'STOP_GAINED' => 2,
'STOP_LOST' => 4,
'COMPLEX_INDEL' => 8,
'FRAMESHIFT_CODING' => 16,
'NON_SYNONYMOUS_CODING' => 32,
'SPLICE_SITE' => 64,
'SYNONYMOUS_CODING' => 128,
'REGULATORY_REGION' => 256,
'WITHIN_MATURE_miRNA' =>512,
'5PRIME_UTR' => 1024,
'3PRIME_UTR' => 2048,
'UTR' => 2094,
'INTRONIC' => 4096,
'WITHIN_NON_CODING_GENE' => 8192,
'UPSTREAM' => 16384,
'DOWNSTREAM' => 32768,
'INTERGENIC' => 65536,
'_' => 65537,
);
=head2 new
Arg [1] : (optional) int $transcript_id
Arg [2] : (optional) int $variation_feature_id
Arg [2] : (optional) int $start
Arg [3] : (optional) int $end
Arg [4] : (optional) int $strand
Arg [5] : (optional) refarray $alleles
Example : $synonym = Bio::EnsEMBL::Variation::ConsequenceType->new($transcript_id,$variation_feature_id,$start,$end,$strand,['A','C']);
Description: Creates a new ConsequenceType
Returntype : Bio::EnsEMBL::Variation::ConsequenceType
Exceptions : none
Caller : general
Status : At Risk
=cut
sub new {
my ($caller, $transcript_id, $variation_feature_id, $start, $end, $strand, $alleles) = @_;
my $class = ref($caller) || $caller;
return bless( {'transcript_id' => $transcript_id,
'variation_feature_id' => $variation_feature_id,
'alleles' => $alleles,
'start' => $start,
'end' => $end,
'strand' => $strand}, $class );
}
=head2 transcript_id
Arg [1] : (optional) int $transcript_id
Example : $transcript_id = $consequence_type->transcript_id;
Description: Getter/Setter for the internal id of the transcript_id calculated
the effect of the Variation
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub transcript_id {
my $self = shift;
if(@_) {
$self->{'transcript_id'} = shift;
}
return $self->{'transcript_id'};
}
=head2 variation_feature_id
Arg [1] : (optional) int $variation_feature_id
Example : $variation_feature_id = $consequence_type->variation_feature_id;
Description: Getter/Setter for the variation_feature affecting the transcript
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub variation_feature_id {
my $self = shift;
if(@_) {
$self->{'variation_feature_id'} = shift;
}
return $self->{'variation_feature_id'};
}
=head2 alleles
Arg [1] : (optional) array ref $alleles
Example : @alleles = @{$consequence_type->alleles};
Description: Getter/Setter for the alleles for the variation
Returntype : reference to array
Exceptions : none
Caller : general
Status : At Risk
=cut
sub alleles {
my $self = shift;
if(@_) {
$self->{'alleles'} = shift;
}
return $self->{'alleles'};
}
=head2 start
Arg [1] : (optional) int $start
Example : $start = $consequence_type->start
Description: Getter/Setter for the start of the variation in the sequence
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub start {
my $self = shift;
if(@_) {
$self->{'start'} = shift;
}
return $self->{'start'}
}
=head2 end
Arg [1] : (optional) int $end
Example : $end = $consequence_type->end
Description: Getter/Setter for the end of the variation in the sequence
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub end {
my $self = shift;
if(@_) {
$self->{'end'} = shift;
}
return $self->{'end'}
}
=head2 strand
Arg [1] : (optional) int $strand
Example : $strand = $consequence_type->strand
Description: Getter/Setter for the strand of the variation in the sequence
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub strand {
my $self = shift;
if(@_) {
$self->{'strand'} = shift;
}
return $self->{'strand'}
}
=head2 aa_start
Arg [1] : (optional) int $aa_start
Example : $aa_start = $consequence_type->aa_start
Description: Getter/Setter for the start of the aa in peptide coordinates
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub aa_start {
my $self = shift;
if(@_) {
$self->{'aa_start'} = shift;
}
return $self->{'aa_start'}
}
=head2 aa_end
Arg [1] : (optional) int $aa_end
Example : $aa_end = $consequence_type->aa_end
Description: Getter/Setter for the end of the aa in peptide coordinates
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub aa_end {
my $self = shift;
if(@_) {
$self->{'aa_end'} = shift;
}
return $self->{'aa_end'}
}
=head2 cdna_start
Arg [1] : (optional) int $cdna_start
Example : $cdna_start = $consequence_type->cdna_start
Description: Getter/Setter for the start of the variation in the cdna coordinates
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub cdna_start {
my $self = shift;
if(@_) {
$self->{'cdna_start'} = shift;
}
return $self->{'cdna_start'}
}
=head2 cdna_end
Arg [1] : (optional) int $cdna_end
Example : $cdna_end = $consequence_type->cdna_end
Description: Getter/Setter for the end of the variation in cdna coordinates
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub cdna_end {
my $self = shift;
if(@_) {
$self->{'cdna_end'} = shift;
}
return $self->{'cdna_end'}
}
=head2 type
Arg [1] : string $type
(possible types 'FRAMESHIFT_CODING','STOP_GAINED','STOP_LOST','NON_SYNONYMOUS_CODING',
'SYNONYMOUS_CODING','REGULATORY_REGION','WITHIN_MATURE_miRNA','5PRIME_UTR','3PRIME_UTR','INTRONIC','UPSTREAM','DOWNSTREAM','WITHIN_NON_CODING_GENE','INTERGENIC', 'SARA')
Example : $consequence_type = $consequence_type->type
Description: Getter/Setter for consequence type of the variation in the transcript
Returntype : none
Exceptions : warning if the consequence type is not recognised
Caller : general
Status : At Risk
=cut
sub type {
my $self = shift;
if(@_) {
my $type = shift;
#there is a special type, SARA, that only applies to the effect of the Alleles, and is equivalent
#to Same As Reference Allele, which is not stored anywhere in the database and need no conversion at all
#when creating the VariationFeature object, thus the absence in the hash
if (defined $CONSEQUENCE_TYPES{$type} || $type eq 'SARA'){
push @{$self->{'type'}}, $type;
}
else{
warning("Trying to set the consequence type to a not valid value. Possible values: ",keys %CONSEQUENCE_TYPES,"\n");
}
}
return $self->{'type'}
}
=head2 aa_alleles
Arg [1] : (optional) string $aa_alleles
Example : $aa_alleles = $consequence_type->aa_alleles
Description: Getter/Setter for the aa that changes in the transcript
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub aa_alleles {
my $self = shift;
if(@_) {
$self->{'aa_alleles'} = shift;
}
return $self->{'aa_alleles'}
}
=head2 codon
Arg [1] : (optional) string $codon
Example : $codon = $consequence_type->codon
Description: Getter/Setter for the codon affected by that Allele in the transcript
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub codon {
my $self = shift;
if(@_) {
$self->{'codon'} = shift;
}
return $self->{'codon'}
}
=head2 cds_start
Arg [1] : (optional) int $cds_start
Example : $cds_start = $consequence_type->cds_start
Description: Getter/Setter for the start of the variation in the coding sequence
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub cds_start {
my $self = shift;
if(@_) {
$self->{'cds_start'} = shift;
}
return $self->{'cds_start'}
}
=head2 cds_end
Arg [1] : (optional) int $cds_end
Example : $cds_end = $consequence_type->cds_end
Description: Getter/Setter for the end of the variation in the coding sequence
Returntype : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub cds_end {
my $self = shift;
if(@_) {
$self->{'cds_end'} = shift;
}
return $self->{'cds_end'}
}
=head2 display_consequence
Arg [1] : (optional) string $consequence_type
Example : $display_consequence = $ct->display_consequence();
Description: Getter for the consequence type to display,
when more than one
Returntype : string
Exceptions : throw on incorrect argument
Caller : webteam
Status : At Risk
=cut
sub display_consequence{
my $self = shift;
my $highest_priority;
#get the value to display from the consequence_type attribute
$highest_priority = 'INTERGENIC';
foreach my $ct (@{$self->type}){
if ($CONSEQUENCE_TYPES{$ct} < $CONSEQUENCE_TYPES{$highest_priority}){
$highest_priority = $ct;
}
}
return $highest_priority;
}
sub empty_type{
my $self = shift;
$self->{'type'} = ();
return $self->type;
}
1;
]]>