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Christopher Fields
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Bio::PopGen::PopulationI - Interface for Populations


  # Get Bio::PopGen::PopulationI object somehow, like
  # from Bio::Population::Population

  print "name is ", $population->name(), "\n";
  print "source is ", $population->source(), "\n";
  print "description is ", $population->description(), "\n";

  print "For marker $markername:\n";
  foreach my $genotype ( $population->get_Genotypes(-marker => $markername) ) {
      print "Individual ", $genotype->individual_id, " genotype alleles are ",
      join(',', $genotype->get_Alleles()), "\n";
  # get a marker with allele frequencies calculated from the population
  my $marker = $population->get_Marker($markername); 
  my %af = $marker->get_Allele_Frequencies;
  foreach my $allele ( keys %af ) {
      print "$allele $af{$allele}\n";


This interface describes the basics of a population. One can use this object to get the genotypes of specific individuals, only those individuals which have a certain marker, or create a marker with allele frequency information.


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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 _


 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   : get_Individuals
 Usage   : my @inds = $pop->get_Individuals();
 Function: Return the individuals, alternatively restrict by a criteria
 Returns : Array of L<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 L<Bio::PopGen::GenotypeI> objects
 Args    : -marker => name of the marker


 Title   : get_Marker
 Usage   : my $marker = $population->get_Marker($name)
 Function: Get a Bio::PopGen::Marker object based on this population
 Returns : L<Bio::PopGen::MarkerI> object
 Args    : 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    : none


 Title   : get_Markers
 Usage   : my @markers = $pop->get_Markers();
 Function: Will retrieve a list of instantiated MarkerI objects 
           for a population.  This is a convience method combining
           get_marker_names with get_Marker
 Returns : List of array of Bio::PopGen::MarkerI objects
 Args    : none


 Title   : get_number_individuals
 Usage   : my $count = $pop->get_number_individuals;
 Function: Get the count of the number of individuals
 Returns : integer >= 0
 Args    : [optional] marker name, will return a count of the number
           of individuals which have this marker