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Bio::PopGen::Genotype(3pm) User Contributed Perl Documentation Bio::PopGen::Genotype(3pm)


Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container


  use Bio::PopGen::Genotype;
  my $genotype = Bio::PopGen::Genotype->new(-marker_name   => $name,
                                           -individual_id => $indid,
                                           -alleles       => \@alleles);


This object will contain alleles for a given marker for a given individual.

The class variable BlankAlleles (accessible through $Bio::PopGen::Genotype::BlankAlleles = 'somepattern') can be set to a regexp pattern for identifying blank alleles which should no be counted (they are effectively missing data). By default it set to match white space, '-', 'N' or 'n', and '?' as blank alleles which are skipped.


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AUTHOR - Jason Stajich



Matthew Hahn,


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 Title   : new
 Usage   : my $obj = Bio::PopGen::Genotype->new();
 Function: Builds a new Bio::PopGen::Genotype object 
 Returns : an instance of Bio::PopGen::Genotype
 Args    : -marker_name   => string representing name of the marker
           -individual_id => string representing individual id (optional)
           -alleles       => arrayref with each item in the array being an allele


 Title   : marker_name
 Usage   : my $name = $genotype->marker_name();
 Function: Get the marker name for a genotype result
 Returns : string
 Args    : [optional] marker name value to store


 Title   : marker_type
 Usage   : my $name = $genotype->marker_type();
 Function: Get the marker type for a genotype result
 Returns : M (microsatellite, or other multi-allelic 
           locus) or S (biallelic/SNP locus)
 Args    : [optional] marker type value to store


 Title   : individual_id
 Usage   : my $indid = $genotype->individual_id();
 Function: Gets the individual id associated with a genotype
           This is effectively a back reference since we will typically
           associate a genotype with an individual with an 
           individual HAS-A genotype relationship.
 Returns : unique id string for an individual
 Args    : none


 Title   : get_Alleles
 Usage   : my @alleles = $genotype->get_Alleles();
 Function: Get the alleles for a given marker and individual
 Returns : array of alleles (strings in this implementation)
 Args    : $showblank - boolean flag to indicate return ALL alleles not 
                        skipping the coded EMPTY alleles
 Note    : Uses the class variable $BlankAlleles to test if alleles
           should be skipped or not.


 Title   : add_Allele
 Usage   : $genotype->add_Allele(@alleles);
 Function: Add alleles to the genotype, at this point there is no
           verification to insure that haploid individuals only have 1 
           allele or that diploids only have 2 - we assume that is
           done by the user creating these objects 
 Returns : count of the number of alleles in genotype
 Args    : Array of alleles to store


 Title   : reset_Alleles
 Usage   : $genotype->reset_Alleles;
 Function: Resets the stored alleles so the list is empty
 Returns : None
 Args    : None
2018-10-27 perl v5.26.2