#
# BioPerl module for Bio::PopGen::Population
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::PopGen::Population - A population of individuals
=head1 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 = $population->get_Marker($name);
}
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;
=head1 DESCRIPTION
This is a collection of individuals. We'll have ways of generating
L<Bio::PopGen::MarkerI> objects out so we can calculate allele_frequencies
for implementing the various statistical tests.
=head1 FEEDBACK
=head2 Mailing Lists
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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
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:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 CONTRIBUTORS
Matthew Hahn, matthew.hahn-at-duke.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::PopGen::Population;
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::PopGen::Marker;
use Bio::PopGen::Genotype;
our $CheckISA = 1;
use base qw(Bio::Root::Root Bio::PopGen::PopulationI);
=head2 new
Title : new
Usage : my $obj = Bio::PopGen::Population->new();
Function: Builds a new Bio::PopGen::Population object
Returns : an instance of Bio::PopGen::Population
Args : -individuals => array ref of individuals (optional)
-name => population name (optional)
-source => a source tag (optional)
-description => a short description string of the population (optional)
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_individuals'} = [];
my ($name,$source,$description,
$inds,$checkisa) = $self->_rearrange([qw(NAME
SOURCE
DESCRIPTION
INDIVIDUALS
CHECKISA)], @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);
$self->{'_checkisa'} = defined $checkisa ? $checkisa : $CheckISA;
return $self;
}
=head2 name
Title : name
Usage : my $name = $pop->name
Function: Get the population name
Returns : string representing population name
Args : [optional] string representing population name
=cut
sub name{
my $self = shift;
return $self->{'_name'} = shift if @_;
return $self->{'_name'};
}
=head2 description
Title : description
Usage : my $description = $pop->description
Function: Get the population description
Returns : string representing population description
Args : [optional] string representing population description
=cut
sub description{
my $self = shift;
return $self->{'_description'} = shift if @_;
return $self->{'_description'};
}
=head2 source
Title : source
Usage : my $source = $pop->source
Function: Get the population source
Returns : string representing population source
Args : [optional] string representing population source
=cut
sub source{
my $self = shift;
return $self->{'_source'} = shift if @_;
return $self->{'_source'};
}
=head2 annotation
Title : annotation
Usage : my $annotation_collection = $pop->annotation;
Function: Get/set a Bio::AnnotationCollectionI for this population
Returns : Bio::AnnotationCollectionI object
Args : [optional set] Bio::AnnotationCollectionI object
=cut
sub annotation{
my ($self, $arg) = @_;
return $self->{_annotation} unless $arg;
$self->throw("Bio::AnnotationCollectionI required for argument") unless
ref($arg) && $arg->isa('Bio::AnnotationCollectionI');
return $self->{_annotation} = $arg;
}
=head2 set_Allele_Frequency
Title : set_Allele_Frequency
Usage : $population->set_Allele_Frequency('marker' => { 'allele1' => 0.1});
Function: Sets an allele frequency for a Marker for this Population
This allows the Population to not have individual individual
genotypes but rather a set of overall allele frequencies
Returns : Count of the number of markers
Args : -name => (string) marker name
-allele => (string) allele name
-frequency => (double) allele frequency - must be between 0 and 1
OR
-frequencies => { 'marker1' => { 'allele1' => 0.01,
'allele2' => 0.99},
'marker2' => ...
}
=cut
sub set_Allele_Frequency {
my ($self,@args) = @_;
my ($name,$allele, $frequency,
$frequencies) = $self->_rearrange([qw(NAME
ALLELE
FREQUENCY
FREQUENCIES
)], @args);
if( defined $frequencies ) { # this supercedes the res
if( ref($frequencies) =~ /HASH/i ) {
my ($markername,$alleles);
while( ($markername,$alleles) = each %$frequencies ) {
$self->{'_allele_freqs'}->{$markername} =
Bio::PopGen::Marker->new(-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} =
Bio::PopGen::Marker->new(-name => $name);
}
$self->{'_allele_freqs'}->{$name}->add_Allele_Frequency($allele,$frequency);
}
return scalar keys %{$self->{'_allele_freqs'}};
}
=head2 add_Individual
Title : add_Individual
Usage : $population->add_Individual(@individuals);
Function: Add individuals to a population
Returns : count of the current number in the object
Args : Array of Individuals
=cut
sub add_Individual{
my ($self,@inds) = @_;
foreach my $i ( @inds ) {
next if ! defined $i;
unless( $self->{'_checkisa'} ? $i->isa('Bio::PopGen::IndividualI') : 1 ) {
$self->warn("cannot add an individual ($i) which is not a Bio::PopGen::IndividualI");
next;
}
}
push @{$self->{'_individuals'}}, @inds;
$self->{'_cached_markernames'} = undef;
$self->{'_allele_freqs'} = {};
return scalar @{$self->{'_individuals'} || []};
}
=head2 remove_Individuals
Title : remove_Individuals
Usage : $population->remove_Individuals(@ids);
Function: Remove individual(s) to a population
Returns : count of the current number in the object
Args : Array of ids
=cut
sub remove_Individuals {
my ($self,@names) = @_;
my $i = 0;
my %namehash; # O(1) lookup will be faster I think
foreach my $n ( @names ) { $namehash{$n}++ }
my @tosplice;
foreach my $ind ( @{$self->{'_individuals'} || []} ) {
unshift @tosplice, $i if( $namehash{$ind->unique_id} );
$i++;
}
foreach my $index ( @tosplice ) {
splice(@{$self->{'_individuals'}}, $index,1);
}
$self->{'_cached_markernames'} = undef;
$self->{'_allele_freqs'} = {};
return scalar @{$self->{'_individuals'} || []};
}
=head2 get_Individuals
Title : get_Individuals
Usage : my @inds = $pop->get_Individuals();
Function: Return the individuals, alternatively restrict by a criteria
Returns : Array of Bio::PopGen::IndividualI objects
Args : none if want all the individuals OR,
-unique_id => To get an individual with a specific id
-marker => To only get individuals which have a genotype specific
for a specific marker name
=cut
sub get_Individuals{
my ($self,@args) = @_;
my @inds = @{$self->{'_individuals'} || []};
return unless @inds;
if( @args ) { # save a little time here if @args is empty
my ($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;
}
=head2 get_Genotypes
Title : get_Genotypes
Usage : my @genotypes = $pop->get_Genotypes(-marker => $name)
Function: Get the genotypes for all the individuals for a specific
marker name
Returns : Array of Bio::PopGen::GenotypeI objects
Args : -marker => name of the marker
=cut
sub get_Genotypes{
my ($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 ();
}
=head2 get_marker_names
Title : get_marker_names
Usage : my @names = $pop->get_marker_names;
Function: Get the names of the markers
Returns : Array of strings
Args : [optional] boolean flag to ignore internal cache status
=cut
sub get_marker_names {
my ($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}++;
}
my @nms = keys %unique;
if( $nms[0] =~ /^(Site|Codon)/ ) {
# sort by site or codon number and do it in
# a schwartzian transformation baby!
@nms = map { $_->[1] }
sort { $a->[0] <=> $b->[0] }
map { [$_ =~ /^(?:Codon|Site)-(\d+)/, $_] } @nms;
}
$self->{'_cached_markernames'} = [ @nms ];
return @{$self->{'_cached_markernames'} || []};
}
=head2 get_Marker
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
=cut
sub get_Marker{
my ($self,$markername) = @_;
my $marker;
# setup some caching too
if( defined $self->{'_allele_freqs'} &&
defined ($marker = $self->{'_allele_freqs'}->{$markername}) ) {
# marker is now set to the stored value
} else {
my @genotypes = $self->get_Genotypes(-marker => $markername);
$marker = Bio::PopGen::Marker->new(-name => $markername);
if( ! @genotypes ) {
$self->warn("No genotypes for Marker $markername in the population");
} else {
my %alleles;
my $count;
for my $al ( map { $_->get_Alleles} @genotypes ) {
next if($al eq '?');
$count++;
$alleles{$al}++
}
foreach my $allele ( keys %alleles ) {
$marker->add_Allele_Frequency($allele, $alleles{$allele}/$count);
$marker->{_marker_coverage} = $count/2;
}
}
$self->{'_allele_freqs'}->{$markername} = $marker;
}
return $marker;
}
=head2 get_number_individuals
Title : get_number_individuals
Usage : my $count = $pop->get_number_individuals;
Function: Get the count of the number of individuals
Returns : integer >= 0
Args : none
=cut
sub get_number_individuals{
my ($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;
}
}
=head2 set_number_individuals
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.
=cut
sub set_number_individuals{
my ($self,$indcount) = @_;
return $self->{'_forced_set_individuals'} = $indcount;
}
=head2 get_Frequency_Homozygotes
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 : $markername
=cut
sub get_Frequency_Homozygotes{
my ($self,$marker,$allelename) = @_;
my ($homozygote_count) = 0;
return 0 if ! defined $marker || ! defined $allelename;
$marker = $marker->name if( defined $marker &&
ref($marker) &&
( $self->{'_checkisa'} ?
$marker->isa('Bio::PopGen::MarkerI') : 1));
my $total = $self->get_number_individuals($marker);
foreach my $genotype ( $self->get_Genotypes($marker) ) {
my %alleles = map { $_ => 1} $genotype->get_Alleles();
# what to do for non-diploid situations?
if( $alleles{$allelename} ) {
$homozygote_count++ if( keys %alleles == 1);
}
}
return $total ? $homozygote_count / $total : 0;
}
=head2 get_Frequency_Heterozygotes
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 : $markername
=cut
sub get_Frequency_Heterozygotes{
my ($self,$marker,$allelename) = @_;
my ($heterozygote_count) = 0;
return 0 if ! defined $marker || ! defined $allelename;
$marker = $marker->name if( defined $marker && ref($marker) &&
($self->{'_checkisa'} ?
$marker->isa('Bio::PopGen::MarkerI') : 1));
if( ref($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();
# what to do for non-diploid situations?
if( $alleles{$allelename} ) {
$heterozygote_count++ if( keys %alleles == 2);
}
}
return $total ? $heterozygote_count / $total : 0;
}
=head2 haploid_population
Title : haploid_population
Usage : my $pop = $population->haploid_population;
Function: Make a new population where all the individuals
are haploid - effectively an individual out of each
chromosome an individual has.
Returns : L<Bio::PopGen::PopulationI>
Args : None
=cut
sub haploid_population{
my ($self) = @_;
my @inds;
my @marker_names = $self->get_marker_names;
for my $ind ( $self->get_Individuals ) {
my @chromosomes;
my $id = $ind->unique_id;
# separate genotypes into 'chromosomes'
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);
}
1;