Bio::EnsEMBL::Variation
AlleleGroup
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Summary
Bio::EnsEMBL::Variation::AlleleGroup - Ensembl representation of a grouping of
alleles (aka haplotype).
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::EnsEMBL::Variation::AlleleGroup;
...
# instantiate a new AlleleGroup
$ag = Bio::EnsEMBL::Variation::AlleleGroup->new
(-name => 'ABDR-20',
-variation_group => $var_group,
-population => $pop,
-source => 'dbSNP',
-frequency => 0.32);
# add some variations and the alleles that make up this group
$ag->add_Variation($var1, 'T');
$ag->add_Variation($var2, 'C');
# print some info about an allele group
print $ag->name(), "\n";
print $ag->variation_group()->name(), "\n";
print $ag->population()->name(), "\n" if($ag->population());
print $ag->source(), "\n";
print $ag->frequency(), "\n" if($ag->frequency());
# print out the names of the variations and the alleles that comprise
# this allele group
$vars = $ag->get_all_Variations();
$alleles = $ag->get_all_alleles();
for($i=0; $i < @$vars; $i++) {
print $vars->[$i]->name(), ':', $alleles->[$i], "\n";
}
Description
This is a class representing a grouping of alleles that have tight linkage and
are usually present together. This is commonly known as a Haplotype or
Haplotype Block.
Methods
Methods description
Arg [1] : Bio::EnsEMBL::Variation::Variation $var
Arg [2] : string $allele
Example : $ag->add_Variation($var2, 'C');
Description: Adds an allele and associated variation to this allele group
Returntype : none
Exceptions : throw on incorrect arguments
Caller : AlleleGroupAdaptor
Status : At Risk |
Arg [1] : (optional) float $freq
Example : print $ag->frequency(), "\n";
Description: Getter/Setter for the frequence of this AlleleGroup
Returntype : float
Exceptions : none
Caller : general
Status : At Risk |
Arg [1] : none
Example :
$vars = $ag->get_all_Variations();
$alleles = $ag->get_all_alleles();
for($i=0; $i < @$vars; $i++) {
print $vars->[$i]->name(), ':', $alleles->[$i], "\n";
}
Description: Retrieves all variations that are associated with the alleles
that comprise this allele group.
The ordering of the Variations returned by this method are
consistant with the ordering of the alleles returned by the
get_all_alleles method. The third allele corresponds to the
third variation, etc.
Returntype : reference to a list of strings
Exceptions : none
Caller : general
Status : At Risk |
Arg [1] : none
Example :
$vars = $ag->get_all_Variations();
$alleles = $ag->get_all_alleles();
for($i=0; $i < @$vars; $i++) {
print $vars->[$i]->name(), ':', $alleles->[$i], "\n";
}
Description: Retrieves all alleles that are part of this allele group.
The alleles are returned as simple strings. The ordering of
the alleles returned by this method are consistant with the
ordering of the variations returned by the get_all_Variations
method. The third allele corresponds to the third variation,
etc.
Returntype : reference to a list of strings
Exceptions : none
Caller : general
Status : At Risk |
Arg [1] : string $name
Example : print $allele_group->name();
Description: Getter/Setter for the name of this AlleleGroup
Returntype : string
Exceptions : none
Caller : general
Status : At Risk |
Arg [dbID] :
int - unique internal identifier for this allele group
Arg [ADAPTOR] :
Bio::EnsEMBL::Variation::DBSQL::AlleleGroupAdaptor
Arg [NAME] :
string - the name of this allele group
Arg [POPULATION] :
Bio::EnsEMBL::Variation::Population - the population this AlleleGroup is
found in.
Arg [SOURCE] :
string - the name of the database this allele group is from
Arg [VARIATION_GROUP] :
Bio::EnsEMBL::Variation::VariationGroup - the horizontal grouping of
variations that this allele group belongs to.
Arg [FREQUENCY] :
The frequency of occurance of this AlleleGroup
Example :
$ag = Bio::EnsEMBL::Variation::AlleleGroup->new
(-name => 'ABDR-20',
-variation_group => $var_group,
-population => $pop,
-source => 'dbSNP',
-frequency => 0.32);
Description: Constructor. Instantiates a new AlleleGroup
Returntype : Bio::EnsEMBL::Variation::AlleleGroup
Exceptions : none
Caller : general
Status : At Risk |
Arg [1] : (optional) Bio::EnsEMBL::Variation::Population $pop
Example : print $ag->population()->name() if($ag->population());
Description: Getter/Setter for the Population associated with this
allele group. Returns undef if there is no population
associated with this allele group
Returntype : Bio::EnsEMBL::Variation::Population
Exceptions : tr
Caller : general
Status : At Risk |
Arg [1] : (optional) string $source
Example : print $ag->source(), "\n";
Description: Getter/Setter for the name of the source database of this
AlleleGroup.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk |
Arg [1] : (optional) Bio::EnsEMBL::Variation::VariationGroup $vg
Example : print $ag->variation_group()->name();
Description: Getter/Setter for VariationGroup associated with this allele
group.
Returntype : Bio::EnsEMBL::Variation::VariationGroup
Exceptions : none
Caller : general
Status : At Risk |
Methods code
sub add_Variation
{ my $self = shift;
my $var = shift;
my $allele = shift;
if(!ref($var) || !$var->isa('Bio::EnsEMBL::Variation::Variation')) {
throw('Bio::EnsEMBL::Variation::Variation argument expected');
}
if(!$allele) {
throw('allele argument expeceted');
}
push @{$self->{'variations'}}, $var;
push @{$self->{'alleles'}}, $allele;
return;
}
1;} | sub frequency
{ my $self = shift;
$self->{'frequency'} = shift if(@_);
return $self->{'frequency'};} | sub get_all_Variations
{ my $self = shift;
return $self->{'variations'};} | sub get_all_alleles
{ my $self = shift;
return $self->{'alleles'};} | sub name
{ my $self = shift;
$self->{'name'} = shift if(@_);
return $self->{'name'};} | sub new
{ my $class = shift;
my ($dbID, $adaptor, $name, $pop, $src, $var_grp, $freq) =
rearrange([qw(DBID ADAPTOR NAME POPULATION
SOURCE VARIATION_GROUP FREQUENCY)], @_);
if(defined($pop) &&
(!ref($pop) || !$pop->isa('Bio::EnsEMBL::Variation::Population'))) {
throw('Bio::EnsEMBL::Variation::Population argument expected');
}
if(defined($var_grp) && (!ref($var_grp) ||
!$var_grp->isa('Bio::EnsEMBL::Variation::VariationGroup'))) {
throw('Bio::EnsEMBL::Variation::VariationGroup argument expected');
}
return bless {'dbID' => $dbID,
'adaptor' => $adaptor,
'name' => $name,
'population' => $pop,
'source' => $src,
'variation_group' => $var_grp,
'frequency' => $freq}, $class;} | sub population
{ my $self = shift;
if(@_) {
my $pop = shift;
if(defined($pop) &&
(!ref($pop) || !$pop->isa('Bio::EnsEMBL::Variation::Population'))) {
throw('Bio::EnsEMBL::Variation::Population argument expected');
}
$self->{'population'} = $pop;
}
return $self->{'population'};} | sub source
{ my $self = shift;
$self->{'source'} = shift if(@_);
return $self->{'source'};} | sub variation_group
{ my $self = shift;
if(@_) {
my $vg = shift;
if(defined($vg) &&
(!ref($vg) || !$vg->isa('Bio::EnsEMBL::Variation::VariationGroup'))) {
throw('Bio::EnsEMBL::Variation::VariationGroup argument expected');
}
$self->{'variation_group'} = $vg
}
return $self->{'variation_group'};} | General documentation