#
# BioPerl module for Bio::PopGen::Genotype
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-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::Genotype - An implementation of GenotypeI which is just an allele container
=head1 SYNOPSIS
use Bio::PopGen::Genotype;
my $genotype = Bio::PopGen::Genotype->new(-marker_name => $name,
-individual_id => $indid,
-alleles => \@alleles);
=head1 DESCRIPTION
This object will contain alleles for a given marker for a given
individual.
The class variable BlankAlleles (accessible through
$Bio::PopGen::Genotype::BlankAlleles = 'somepattern') can be set to a
regexp pattern for identifying blank alleles which should no be
counted (they are effectively missing data). By default it set to
match white space, '-', 'N' or 'n', and '?' as blank alleles which are
skipped.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 CONTRIBUTORS
Matthew Hahn, matthew.hahn-at-duke.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::PopGen::Genotype;
use vars qw($BlankAlleles);
use strict;
$BlankAlleles = '[\s\-Nn\?]';
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::Root::Root Bio::PopGen::GenotypeI);
=head2 new
Title : new
Usage : my $obj = Bio::PopGen::Genotype->new();
Function: Builds a new Bio::PopGen::Genotype object
Returns : an instance of Bio::PopGen::Genotype
Args : -marker_name => string representing name of the marker
-individual_id => string representing individual id (optional)
-alleles => arrayref with each item in the array being an allele
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($marker_name, $marker_type, $ind_id, $alleles) = $self->_rearrange([qw(MARKER_NAME
MARKER_TYPE
INDIVIDUAL_ID
ALLELES)],@args);
defined $marker_name && $self->marker_name($marker_name);
defined $marker_type && $self->marker_type($marker_type);
defined $ind_id && $self->individual_id($ind_id);
if( defined $alleles ) {
if( ref($alleles) =~ /array/i ) {
$self->add_Allele(@$alleles);
} else {
$self->warn("Could not initialize with -alleles value, it is not an array ref");
}
}
return $self;
}
=head2 marker_name
Title : marker_name
Usage : my $name = $genotype->marker_name();
Function: Get the marker name for a genotype result
Returns : string
Args : [optional] marker name value to store
=cut
sub marker_name{
my ($self) = shift;
return $self->{'_marker_name'} = shift if @_;
return $self->{'_marker_name'};
}
=head2 marker_type
Title : marker_type
Usage : my $name = $genotype->marker_type();
Function: Get the marker type for a genotype result
Returns : M (microsatellite, or other multi-allelic
locus) or S (biallelic/SNP locus)
Args : [optional] marker type value to store
=cut
sub marker_type{
my ($self) = shift;
return $self->{'_marker_type'} = shift if @_;
return $self->{'_marker_type'};
}
=head2 individual_id
Title : individual_id
Usage : my $indid = $genotype->individual_id();
Function: Gets the individual id associated with a genotype
This is effectively a back reference since we will typically
associate a genotype with an individual with an
individual HAS-A genotype relationship.
Returns : unique id string for an individual
Args : none
=cut
sub individual_id {
my ($self) = shift;
return $self->{'_individual_id'} = shift if @_;
return $self->{'_individual_id'};
}
=head2 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 $BlankAlleles to test if alleles
should be skipped or not.
=cut
sub get_Alleles{
my ($self) = shift;
if( @_ && $_[0] ) {
return @{$self->{'_alleles'} || []};
} else {
if( defined $self->{'_cached_noblank'} ) {
return @{$self->{'_cached_noblank'}}
}
# one liners - woo hoo.
$self->{'_cached_noblank'} = [ grep { ! /^\s*$BlankAlleles\s*$/o }
@{$self->{'_alleles'} || []}];
return @{$self->{'_cached_noblank'}};
}
}
=head2 add_Allele
Title : add_Allele
Usage : $genotype->add_Allele(@alleles);
Function: Add alleles to the genotype, at this point there is no
verification to insure that haploid individuals only have 1
allele or that diploids only have 2 - we assume that is
done by the user creating these objects
Returns : count of the number of alleles in genotype
Args : Array of alleles to store
=cut
sub add_Allele {
my ($self) = shift;
$self->{'_cached_noblank'} = undef;
push @{$self->{'_alleles'}}, @_;
return scalar @{$self->{'_alleles'}};
}
=head2 reset_Alleles
Title : reset_Alleles
Usage : $genotype->reset_Alleles;
Function: Resets the stored alleles so the list is empty
Returns : None
Args : None
=cut
sub reset_Alleles{
my ($self,@args) = @_;
$self->{'_cached_noblank'} = undef;
$self->{'_alleles'} = [];
return 0;
}
1;