NAME

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

SYNOPSIS

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

DESCRIPTION

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.

FEEDBACK

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

Support

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 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 the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

Matthew Hahn, matthew.hahn-at-duke.edu

APPENDIX

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

new

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

marker_name

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

marker_type

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

individual_id

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

get_Alleles

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.

add_Allele

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

reset_Alleles

Title   : reset_Alleles
Usage   : $genotype->reset_Alleles;
Function: Resets the stored alleles so the list is empty
Returns : None
Args    : None

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq