NAME

Bio::PopGen::Individual - An implementation of an Individual who has Genotype or Sequence Results

SYNOPSIS

use Bio::PopGen::Individual;

my $ind = Bio::PopGen::Individual->new(-unique_id => $id,
                                      -genotypes => \@genotypes);

DESCRIPTION

This object is a container for genotypes.

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::Individual->new();
Function: Builds a new Bio::PopGen::Individual object 
Returns : an instance of Bio::PopGen::Individual
Args    : -unique_id => $id,
          -genotypes => \@genotypes

unique_id

Title   : unique_id
Usage   : my $id = $individual->unique_id
Function: Unique Identifier
Returns : string representing unique identifier
Args    : string

num_of_results

Title   : num_of_results
Usage   : my $count = $person->num_results;
Function: returns the count of the number of Results for a person
Returns : integer
Args    : none

annotation

Title   : annotation
Usage   : my $annotation_collection = $ind->annotation;
Function: Get/set a Bio::AnnotationCollectionI for this individual
Returns : Bio::AnnotationCollectionI object
Args    : [optional set] Bio::AnnotationCollectionI object

add_Genotype

Title   : add_Genotype
Usage   : $individual->add_Genotype
Function: add a genotype value
Returns : count of the number of genotypes associated with this individual
Args    : @genotypes - L<Bio::PopGen::GenotypeI> object(s) containing 
                       alleles plus a marker name

reset_Genotypes

Title   : reset_Genotypes
Usage   : $individual->reset_Genotypes;
Function: Reset the genotypes stored for this individual
Returns : none
Args    : none

remove_Genotype

Title   : remove_Genotype
Usage   : $individual->remove_Genotype(@names)
Function: Removes the genotypes for the requested markers
Returns : none
Args    : Names of markers 

get_Genotypes

Title   : get_Genotypes
Usage   : my @genotypes = $ind->get_Genotypes(-marker => $markername);
Function: Get the genotypes for an individual, based on a criteria
Returns : Array of genotypes
Args    : either none (return all genotypes) or 
          -marker => name of marker to return (exact match, case matters)

has_Marker

Title   : has_Marker
Usage   : if( $ind->has_Marker($name) ) {}
Function: Boolean test to see if an Individual has a genotype 
          for a specific marker
Returns : Boolean (true or false)
Args    : String representing a marker name

get_marker_names

Title   : get_marker_names
Usage   : my @names = $individual->get_marker_names;
Function: Returns the list of known marker names
Returns : List of strings
Args    : none

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq