Bio::PopGen::Simulation GeneticDrift
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Summary
Bio::PopGen::Simulation::GeneticDrift - A simple genetic drift simulation
Package variables
No package variables defined.
Included modules
Bio::PopGen::Population
Inherit
Bio::Root::Root
Synopsis
  use Bio::PopGen::Simulation::GeneticDrift;
my $sim = Bio::PopGen::Simulation::GeneticDrift->new(-popsize => 40,
-alleles => {A => 0.2,
B => 0.8});
for(my $i =0 ;$i < 10; $i++ ) {
my %f = $sim->next_generation; # get the freqs for each generation
}
for(my $i =0 ;$i < 10; $i++ ) { # get the allele freqs as part of a Bio::PopGen::Population object my $pop = $sim->next_generation('population'); }
Description
A very simple 1 locus multi-allele random drift module, start with an
initial set of allele frequency and simulate what happens over time.
This isn't really useful for anything in particular yet but will be
built upon.
See Gillespie JH. (1998) "Population Genetics: a Concise guide." The Johns
Hopkins University Press, Baltimore, USA. pp.19-47.
Methods
newDescriptionCode
next_generationDescriptionCode
population_sizeDescriptionCode
set_Frequencies_EquivalentDescriptionCode
get_Allele_FrequenciesDescriptionCode
add_Allele_FrequencyDescriptionCode
reset_allelesDescriptionCode
validate_FrequenciesDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::PopGen::Simulation::GeneticDrift->new();
Function: Builds a new Bio::PopGen::Simulation::GeneticDrift object
Returns : an instance of Bio::PopGen::Simulation::GeneticDrift
Args : -popsize => starting N
-haploid => boolean if we should simulate haploids
-alleles => arrayref of the allele names
OR
-population => Bio::PopGen::PopulationI object to initialize
from some previously defined Population object
(or result from a previous simulation)
next_generationcodeprevnextTop
 Title   : next_generation
Usage : my %generation = $sim->next_generation
Function: Get the next generation of allele frequencies based on the current
generation
Returns : Hash of allele frequencies
Args : 'allelefreqs' or 'population' to get back a hash of allele
frequencies (default) OR a Bio::PopGen::Population object
population_sizecodeprevnextTop
 Title   : population_size
Usage : $obj->population_size($newval)
Function:
Example :
Returns : value of population_size (a scalar)
Args : on set, new value (a scalar or undef, optional)
set_Frequencies_EquivalentcodeprevnextTop
 Title   : set_Frequencies_Equivalent
Usage : $sim->set_Frequencies_Equivalent
Function: Reset the allele frequencies so they are all even
Returns : none
Args : none
get_Allele_FrequenciescodeprevnextTop
 Title   : get_Allele_Frequencies
Usage : my %allele_freqs = $marker->get_Allele_Frequencies;
Function: Get the alleles and their frequency (set relative to
a given population - you may want to create different
markers with the same name for different populations
with this current implementation
Returns : Associative array where keys are the names of the alleles
Args : none
add_Allele_FrequencycodeprevnextTop
 Title   : add_Allele_Frequency
Usage : $marker->add_Allele_Frequency($allele,$freq)
Function: Adds an allele frequency
Returns : None
Args : $allele - allele name
$freq - frequency value
reset_allelescodeprevnextTop
 Title   : reset_alleles
Usage : $marker->reset_alleles();
Function: Reset the alleles for a marker
Returns : None
Args : None
validate_FrequenciescodeprevnextTop
 Title   : validate_Frequencies
Usage : if( $sim->validate_Frequencies) {}
Function: Sanity checker that allele frequencies sum to 1 or less
Returns : boolean
Args : -strict => 1 boolean if you want to insure that sum of freqs is 1
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($population,
      $popsize, $haploid, $alleles) = $self->_rearrange([qw(POPULATION
							    POPSIZE
							    HAPLOID
							    ALLELES)],@args);
  if( defined $population && ref($population) &&
      $population->isa('Bio::PopGen::PopulationI') ) {
      $self->population_size($population->get_number_individuals || $popsize);
      my %f = $population->get_Allele_Frequencies;
      while( my ($allele,$freq) = each %f ) {
	  $self->add_Allele_Frequency($allele,$freq);
      }
  } else { 
      $self->population_size($popsize);  
  
      if( ! defined $alleles || ref($alleles) !~ /HASH/i  ) {
	  $self->throw("Must provide a valid set of initial allele frequencies to $class as an hashref");
      } 
      while( my ($allele,$freq) = each %$alleles ) {
	  $self->add_Allele_Frequency($allele,$freq);
      }
  }
  unless( $self->validate_Frequencies ) {
      $self->throw("You specified allele frequencies which summed to more than 1");
  }
  return $self;
}
next_generationdescriptionprevnextTop
sub next_generation {
   my ($self,$rettype) = @_;
   my %initial = $self->get_Allele_Frequencies;
   my $popsize = $self->population_size || 
       $self->throw("Need to have set a valid population size when running the simulation");
   # we're going to construct a mapping of the rational space from 0->1 
# which will map to a particular allele and be proportional to it
# frequency
my ($last,@mapping) = (0); # we'll make ranges that cover from >= left and < right in terms of the
# order doesn't matter - 'distance' does
# range that we're going to try and match
# since rand() goes from 0 up to 1 (not including 1)
foreach my $a ( keys %initial ) { push @mapping, [$last,$initial{$a}+$last,$a]; $last += $initial{$a}; } my %f; for( my $i =0; $i < $popsize; $i++ ) { my $rand = rand(1); foreach my $val ( @mapping ) { if( $rand >= $val->[0] && $rand < $val->[1] ) { $f{$val->[2]}++; last; } } } foreach my $f ( values %f ) { $f /= $popsize;
} %{$self->{'_allele_freqs'}} = %f; if( defined $rettype && $rettype =~ /population/i) { return Bio::PopGen::Poulation->new(-frequencies =>\% f); } else { return %f; }
}
population_sizedescriptionprevnextTop
sub population_size {
    my $self = shift;

    return $self->{'_population_size'} = shift if @_;
    return $self->{'_population_size'};
}
set_Frequencies_EquivalentdescriptionprevnextTop
sub set_Frequencies_Equivalent {
   my ($self) = @_;
   my @alleles = keys %{$self->{'_allele_freqs'}};
   my $eqfreq  = 1 / scalar @alleles;
for ( @alleles ) { $self->{'_allele_freqs'}->{$_} = $eqfreq } return;
}
get_Allele_FrequenciesdescriptionprevnextTop
sub get_Allele_Frequencies {
   return %{$_[0]->{'_allele_freqs'}};
}
add_Allele_FrequencydescriptionprevnextTop
sub add_Allele_Frequency {
   my ($self,$allele,$freq) = @_;
   $self->{'_allele_freqs'}->{$allele} = $freq;
}
reset_allelesdescriptionprevnextTop
sub reset_alleles {
   my ($self) = @_;
   $self->{'_allele_freqs'} = {};
}
validate_FrequenciesdescriptionprevnextTop
sub validate_Frequencies {
   my ($self,@args) = @_;
   my ($strict) = $self->_rearrange([qw(STRICT)], @args);
   my $sum = 0;
   my %freq = $self->get_Allele_Frequencies;
   foreach my $f ( values %freq ) { 
       $sum += $f;
   }
   return ($strict) ? $sum == 1 : $sum <= 1;
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _