Bio::EnsEMBL::Variation
Population
Toolbar
Summary
Bio::EnsEMBL::Variation::Population - A population represents a phenotypic
group, ethnic group, set of individuals used in an assay, etc.
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# Population
$pop = Bio::EnsEMBL::Variation::Population->new
(-name => 'WEST AFRICA',
-description => 'Sub-Saharan Nations bordering Atlantic north' .
' of Congo River, and Central/Southern Atlantic' .
' Island Nations.');
...
# print out all sub populations of a population
# same could work for super populations
print_sub_pops($pop);
sub print_sub_pops {
my $pop = shift;
my $level = shift || 0;
my $sub_pops = $pop->get_all_sub_Populations();
foreach my $sp (@$sub_pops) {
print ' ' x $level++,
'name: ', $sp->name(),
'desc: ', $sp->description(),
'size: ', $sp->size(),"\n";
print_sub_pops($sp, $level);
}
}
Description
This is a class representing a population. A population may consist of any
grouping of individuals, including phenotypic groups (e.g. people with
diabetes), ethnic groups (e.g. caucasians), individuals used in an assay
(e.g. subjects in experiment X), etc.
Populations may be arranged into an arbitrary hierarchy of sub and super
populations.
Methods
Methods description
Arg [1] : Bio::EnsEMBL::Variation::Population $pop
Example : $pop->add_sub_Population($sub_pop);
$sub_pop->add_super_Population($pop);
Description: Adds a sub population to this population.
Returntype : none
Exceptions : throw on incorrect argument
Caller : general
Status : At Risk |
Arg [1] : none
Example : foreach my $sub_pop (@{$pop->get_all_sub_Populations}) {
my $sub_sub_pops = $sub_pop->get_all_sub_Populations();
}
Description: Retrieves all populations which are conceptually a sub set
of this population.
Returntype : reference to list of Bio::EnsEMBL::Variation::Population objects
Exceptions : none
Caller : general
Status : At Risk |
Arg [1] : none
Example : foreach my $sup_pop (@{$pop->get_all_super_Populations}) {
my $sup_sup_pops = $sup_pop->get_all_super_Populations();
}
Description: Retrieves all populations which this population is a part of
from the database.
Super populations may not be directly added in order to avoid
circular references and memory leaks. You must add
sub_Populations instead and store this in the database.
Returntype : reference to list of Bio::EnsEMBL::Variation::Population objects
Exceptions : none
Caller : general
Status : At Risk |
Arg [1] : (optional) string $source - the source of the synonyms to
return.
Example : @dbsnp_syns = @{$p->get_all_synonyms('dbSNP')};
@all_syns = @{$p->get_all_synonyms()};
Description: Retrieves synonyms for this Population. If a source argument
is provided all synonyms from that source are returned,
otherwise all synonyms are returned.
Returntype : reference to list of strings
Exceptions : none
Caller : general
Status : At Risk |
Arg [-dbID]: int - unique internal identifier of the sample
Arg [-ADAPTOR]: Bio::EnsEMBL::PopulationAdaptor
Arg [-NAME]: string - name of the population
Arg [-DESCRIPTION]: string - description of the population
Arg [-SIZE]: int - the size of the population
Arg [-SUB_POPULATIONS]: listref of Bio::EnsEMBL::Population objects
Example : $pop = Bio::EnsEMBL::Variation::Population->new
(-name => 'WEST AFRICA',
-description => 'Sub-Saharan Nations bordering Atlantic north' .
' of Congo River, and Central/Southern Atlantic' .
' Island Nations.'
-sub_populations => \@sub_pops);
Description: Constructor. Instantiates a new Population object
Returntype : Bio::EnsEMBL::Variation::Population
Exceptions : none
Caller : general
Status : At Risk |
Methods code
sub add_sub_Population
{ my $self = shift;
my $pop = shift;
if(!ref($pop) || !$pop->isa('Bio::EnsEMBL::Variation::Population')) {
throw('Bio::EnsEMBL::Variation::Population argument expected.');
}
if($pop == $self) {
throw("Cannot add self as sub population.");
}
$self->{'sub_populations'} ||= [];
push @{$self->{'sub_populations'}}, $pop;
return $pop;} | sub get_all_sub_Populations
{ my $self = shift;
if(!defined($self->{'sub_populations'}) && $self->{'adaptor'}) {
$self->{'sub_populations'} =
$self->{'adaptor'}->fetch_all_by_super_Population($self);
}
return $self->{'sub_populations'} || [];} | sub get_all_super_Populations
{ my $self = shift;
return [] if(!$self->{'adaptor'});
return $self->{'adaptor'}->fetch_all_by_sub_Population($self);} | sub get_all_synonyms
{ my $self = shift;
my $source = shift;
return [] if(!$self->adaptor());
return $self->adaptor()->fetch_synonyms($self->dbID(),$source);
}
1; } | sub new
{ my $caller = shift;
my $class = ref($caller) || $caller;
my ($dbID, $adaptor, $name, $desc, $size, $is_strain, $sub_pops) =
rearrange(['DBID','ADAPTOR','NAME', 'DESCRIPTION', 'SIZE',
'SUB_POPULATIONS'], @_);
return bless {'dbID' => $dbID,
'adaptor' => $adaptor,
'name' => $name,
'description' => $desc,
'size' => $size,
'sub_populations' => $sub_pops}, $class;} | General documentation