Bio::PopGen
Population
Summary
Bio::PopGen::Population - A population of individuals
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
Give standard usage here
Description
This is a collection of individuals. We'll have ways of generating
Bio::PopGen::Marker objects out so we can calculate allele_frequencies
for implementing the various statistical tests.
Methods
Methods description
Title : new
Usage : my $obj = new Bio::PopGen::Population();
Function: Builds a new Bio::PopGen::Population object
Returns : an instance of Bio::PopGen::Population
Args : -individuals => array ref of individuals (optional)
-name => population name (optional)
-source => a source tag (optional)
-description => a short description string of the population (optional) |
Title : name
Usage : my $name = $pop->name
Function: Get the population name
Returns : string representing population name
Args : [optional] string representing population name |
Title : description
Usage : my $description = $pop->description
Function: Get the population description
Returns : string representing population description
Args : [optional] string representing population description |
Title : source
Usage : my $source = $pop->source
Function: Get the population source
Returns : string representing population source
Args : [optional] string representing population source |
Title : set_Allele_Frequency
Usage : $population->set_Allele_Frequency(
Function: Sets an allele frequency for a Marker for this Population
This allows the Population to not have individual individual
genotypes but rather a set of overall allele frequencies
Returns : Count of the number of markers
Args : -name => (string) marker name
-allele => (string) allele name
-frequency => (double) allele frequency - must be between 0 and 1
OR
-frequencies => { 'marker1' => { 'allele1' => 0.01,
'allele2' => 0.99},
'marker2' => ...
} |
Title : add_Individual
Usage : $population->add_Individual(@individuals);
Function: Add individuals to a population
Returns : count of the current number in the object
Args : Array of Individuals |
Title : remove_Individuals
Usage : $population->remove_Individuals(@ids);
Function: Remove individual(s) to a population
Returns : count of the current number in the object
Args : Array of ids |
Title : get_Individuals
Usage : my @inds = $pop->get_Individuals();
Function: Return the individuals, alternatively restrict by a criteria
Returns : Array of Bio::PopGen::IndividualI objects
Args : none if want all the individuals OR,
-unique_id => To get an individual with a specific id
-marker => To only get individuals which have a genotype specific
for a specific marker name |
Title : get_Genotypes
Usage : my @genotypes = $pop->get_Genotypes(-marker => $name)
Function: Get the genotypes for all the individuals for a specific
marker name
Returns : Array of Bio::PopGen::GenotypeI objects
Args : -marker => name of the marker |
Title : get_marker_names
Usage : my @names = $pop->get_marker_names;
Function: Get the names of the markers
Returns : Array of strings
Args : [optional] boolean flag to ignore internal cache status |
Title : get_Marker
Usage : my $marker = $population->get_Marker($name)
Function: Get a Bio::PopGen::Marker object based on this population
Returns : Bio::PopGen::MarkerI object
Args : name of the marker |
Title : get_number_individuals
Usage : my $count = $pop->get_number_individuals;
Function: Get the count of the number of individuals
Returns : integer >= 0
Args : none |
Title : set_number_individuals
Usage : $pop->set_number_individuals($num);
Function: Fixes the number of individuals, call this with
0 to unset.
Only use this if you know what you are doing,
this is only relavent when you are just adding
allele frequency data for a population and want to
calculate something like theta
Returns : none
Args : individual count, calling it with undef or 0
will reset the value to return a number
calculated from the number of individuals
stored for this population. |
Title : get_Frequency_Homozygotes
Usage : my $freq = $pop->get_Frequency_Homozygotes;
Function: Calculate the frequency of homozygotes in the population
Returns : fraction between 0 and 1
Args : $markername |
Title : get_Frequency_Heterozygotes
Usage : my $freq = $pop->get_Frequency_Homozygotes;
Function: Calculate the frequency of homozygotes in the population
Returns : fraction between 0 and 1
Args : $markername |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_individuals'} = [];
my ($name,$source,$description,
$inds) = $self->_rearrange([qw(NAME
SOURCE
DESCRIPTION
INDIVIDUALS)], @args);
if( defined $inds ) {
if( ref($inds) !~ /ARRAY/i ) {
$self->warn("Need to provide a value array ref for the -individuals initialization flag");
} else {
$self->add_Individual(@$inds);
}
}
defined $name && $self->name($name);
defined $source && $self->source($source);
defined $description && $self->description($description);
return $self;} | sub name
{ my $self = shift;
return $self->{'_name'} = shift if @_;
return $self->{'_name'};} | sub description
{ my $self = shift;
return $self->{'_description'} = shift if @_;
return $self->{'_description'};} | sub source
{ my $self = shift;
return $self->{'_source'} = shift if @_;
return $self->{'_source'};} | sub set_Allele_Frequency
{ my ($self,@args) = @_;
my ($name,$allele, $frequency,
$frequencies) = $self->_rearrange([qw(NAME
ALLELE
FREQUENCY
FREQUENCIES
)], @args);
if( defined $frequencies ) {
if( ref($frequencies) =~ /HASH/i ) {
my ($markername,$alleles);
while( ($markername,$alleles) = each %$frequencies ) {
$self->{'_allele_freqs'}->{$markername} =
new Bio::PopGen::Marker(-name => $markername,
-allele_freq => $alleles);
}
} else {
$self->throw("Must provide a valid hashref for the -frequencies option");
}
} else {
unless( defined $self->{'_allele_freqs'}->{$name} ) {
$self->{'_allele_freqs'}->{$name} =
new Bio::PopGen::Marker(-name => $name);
}
$self->{'_allele_freqs'}->{$name}->add_Allele_Frequency($allele,$frequency);
}
return scalar keys %{$self->{'_allele_freqs'}};} | sub add_Individual
{ my ($self,@inds) = @_;
foreach my $i ( @inds ) {
next if ! defined $i;
unless( $i->isa('Bio::PopGen::IndividualI') ) {
$self->warn("cannot add an individual ($i) which is not a Bio::PopGen::IndividualI");
next;
}
push @{$self->{'_individuals'}}, $i;
}
$self->{'_cached_markernames'} = undef;
$self->{'_allele_freqs'} = {};
return scalar @{$self->{'_individuals'}};} | sub remove_Individuals
{ my ($self,@names) = @_;
my $i = 0;
my %namehash;
foreach my $n ( @names ) { $namehash{$n}++ }
my @tosplice;
foreach my $ind ( @{$self->{'_individuals'}} ) {
unshift @tosplice, $i if( $namehash{$ind->person_id} );
$i++;
}
foreach my $index ( @tosplice ) {
splice(@{$self->{'_individuals'}}, $index,1);
}
$self->{'_cached_markernames'} = undef;
$self->{'_allele_freqs'} = {};
return scalar @{$self->{'_individuals'}};} | sub get_Individuals
{ my ($self,@args) = @_;
my @inds = @{$self->{'_individuals'}};
return unless @inds;
if( @args ) {
my ($id,$marker) = $self->_rearrange([qw(UNIQUE_ID MARKER)], @args);
if( defined $id ) {
@inds = grep { $_->unique_id eq $id } @inds;
} elsif (defined $marker) {
@inds = grep { $_->has_Marker($marker) } @inds;
}
}
return @inds;} | sub get_Genotypes
{ my ($self,@args) = @_;
my ($name) = $self->_rearrange([qw(MARKER)],@args);
if( defined $name ) {
return grep { defined $_ } map { $_->get_Genotypes(-marker => $name) }
@{$self->{'_individuals'}}
}
$self->warn("You needed to have provided a valid -marker value");
return ();} | sub get_marker_names
{ my ($self,$force) = @_;
return @{$self->{'_cached_markernames'}}
if( ! $force && defined $self->{'_cached_markernames'});
my %unique;
foreach my $n ( map { $_->get_marker_names } $self->get_Individuals() ) {
$unique{$n}++;
}
$self->{'_cached_markernames'} = [ keys %unique ];
return @{$self->{'_cached_markernames'} };} | sub get_Marker
{ my ($self,$markername) = @_;
my $marker;
if( defined $self->{'_allele_freqs'} &&
defined ($marker = $self->{'_allele_freqs'}->{$markername}) ) {
} else {
my @genotypes = $self->get_Genotypes(-marker => $markername);
$marker = new Bio::PopGen::Marker(-name => $markername);
if( ! @genotypes ) {
$self->warn("No genotypes for Marker $markername in the population");
} else {
my %alleles;
my $count;
map { $count++; $alleles{$_}++ } map { $_->get_Alleles } @genotypes;
foreach my $allele ( keys %alleles ) {
$marker->add_Allele_Frequency($allele, $alleles{$allele}/$count);
}
}
$self->{'_allele_freqs'}->{$markername} = $marker;
}
return $marker; } | sub get_number_individuals
{ my ($self,$markername) = @_;
if( $self->{'_forced_set_individuals'} ) {
return $self->{'_forced_set_individuals'};
}
unless( defined $markername ) {
return scalar @{$self->{'_individuals'}};
} else {
my $number =0;
foreach my $individual ( @{$self->{'_individuals'}} ) {
$number++ if( $individual->has_Marker($markername));
}
return $number;
}} | sub set_number_individuals
{ my ($self,$indcount) = @_;
return $self->{'_forced_set_individuals'} = $indcount;} | sub get_Frequency_Homozygotes
{ my ($self,$marker,$allelename) = @_;
my ($homozygote_count) = 0;
return 0 if ! defined $marker || ! defined $allelename;
$marker = $marker->name if( defined $marker &&
ref($marker) &&
$marker->isa('Bio::PopGen::MarkerI'));
my $total = $self->get_number_individuals($marker);
foreach my $genotype ( $self->get_Genotypes($marker) ) {
my %alleles = map { $_ => 1} $genotype->get_Alleles();
if( $alleles{$allelename} ) {
$homozygote_count++ if( keys %alleles == 1);
}
}
return $total ? $homozygote_count / $total : 0;
} | sub get_Frequency_Heterozygotes
{ my ($self,$marker,$allelename) = @_;
my ($heterozygote_count) = 0;
return 0 if ! defined $marker || ! defined $allelename;
$marker = $marker->name if( defined $marker && ref($marker) &&
$marker->isa('Bio::PopGen::MarkerI'));
if( ref($marker) ) {
$self->warn("Passed in a ".ref($marker). " to has_Marker, expecting either a string or a Bio::PopGen::MarkerI");
return 0;
}
my $total = $self->get_number_individuals($marker);
foreach my $genotype ( $self->get_Genotypes($marker) ) {
my %alleles = map { $_ => 1} $genotype->get_Alleles();
if( $alleles{$allelename} ) {
$heterozygote_count++ if( keys %alleles == 2);
}
}
return $total ? $heterozygote_count / $total : 0;
} | General documentation
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http://bugzilla.bioperl.org/
| AUTHOR - Jason Stajich | Top |
Email jason-at-bioperl.org
Matthew Hahn, matthew.hahn-at-duke.edu
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _