Bio::PopGen
Population
Summary
Bio::PopGen::Population - A population of individuals
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::PopGen::Population;
use Bio::PopGen::Individual;
my $population = Bio::PopGen::Population->new();
my $ind = Bio::PopGen::Individual->new(-unique_id => 'id');
$population->add_Individual($ind);
for my $ind ( $population->get_Individuals ) {
# iterate through the individuals
}
for my $name ( $population->get_marker_names ) {
my $marker = $population->get_Marker();
}
my $num_inds = $population->get_number_individuals;
my $homozygote_f = $population->get_Frequency_Homozygotes;
my $heterozygote_f = $population->get_Frequency_Heterozygotes;
# make a population haploid by making fake chromosomes through
# haplotypes -- ala allele 1 is on chrom 1 and allele 2 is on chrom 2
# the number of individuals created will thus be 2 x number in
# population
my $happop = $population->haploid_population;
Description
This is a collection of individuals. We'll have ways of generating
Bio::PopGen::MarkerI 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('marker' => { 'allele1' => 0.1});
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 |
Title : haploid_population
Usage : my $pop = $population->haploid_population;
Function: Make a new population where all the individuals
are haploid - effectively an individual out of each
chromosome an individual has.
Returns : Bio::PopGen::PopulationI
Args : None |
Methods code
sub new
{ my($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 / $total : 0;
} | sub haploid_population
{ my ($self) = @_;
my @inds;
my @marker_names = $self->get_marker_names;
for my $ind ( $self->get_Individuals ) {
my @chromosomes;
my $id = $ind->unique_id;
for my $marker_name( @marker_names ) {
my ($genotype) = $ind->get_Genotypes(-marker => $marker_name);
my $i =0;
for my $allele ( $genotype->get_Alleles ) {
push @{$chromosomes[$i]},
Bio::PopGen::Genotype->new(-marker_name => $marker_name,
-individual_id => $id.".$i",
-alleles => [$allele]);
$i++;
}
}
for my $chrom ( @chromosomes ) {
my $copyind = ref($ind)->new(-unique_id => $id.".1",
-genotypes => $chrom);
push @inds, $ind;
}
}
my $population = ref($self)->new(-name => $self->name,
-source => $self->source,
-description => $self->description,
-individuals =>\@ inds);} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
http://bugzilla.open-bio.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 _