Bio::PopGen
Genotype
Toolbar
Summary
Bio::PopGen::Genotype - An implementation of GenotypeI which is just an allele container
Package variables
No package variables defined.
Inherit
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.
Methods
Methods description
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 : $genotype->reset_Alleles;
Function: Resets the stored alleles so the list is empty
Returns : None
Args : None |
Methods code
sub new
{ my($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 $self;} | sub marker_name
{ my ($self) = shift;
return $self->{'_marker_name'} = shift if @_;
return $self->{'_marker_name'};} | sub marker_type
{ my ($self) = shift;
return $self->{'_marker_type'} = shift if @_;
return $self->{'_marker_type'};} | sub individual_id
{ my ($self) = shift;
return $self->{'_individual_id'} = shift if @_;
return $self->{'_individual_id'};} | sub get_Alleles
{ my ($self) = shift;
if( @_ && $_[0] ) {
return @{$self->{'_alleles'} || []};
} else {
if( defined $self->{'_cached_noblank'} ) {
return @{$self->{'_cached_noblank'}}
}
$self->{'_cached_noblank'} = [ grep { ! /^\s*$BlankAlleles\s*$/o }
@{$self->{'_alleles'} || []}];
return @{$self->{'_cached_noblank'}};
}} | sub add_Allele
{ my ($self) = shift;
$self->{'_cached_noblank'} = undef;
push @{$self->{'_alleles'}}, @_;
return scalar @{$self->{'_alleles'}};} | sub reset_Alleles
{ my ($self,@args) = @_;
$self->{'_cached_noblank'} = undef;
$self->{'_alleles'} = [];
return 0;
}
1;} | General documentation
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
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.
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/
| AUTHOR - Jason Stajich | Top |
Email jason-at-bioperl.org
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 _