Ewan Birney

NAME

Bio::Species - Generic species object

SYNOPSIS

    $species = Bio::Species->new(-classification => [@classification]);
                                    # Can also pass classification
                                    # array to new as below

    $species->classification(qw( sapiens Homo Hominidae
                                 Catarrhini Primates Eutheria
                                 Mammalia Vertebrata Chordata
                                 Metazoa Eukaryota ));

    $genus = $species->genus();

    $bi = $species->binomial();     # $bi is now "Homo sapiens"

    # For storing common name
    $species->common_name("human");

    # For storing subspecies
    $species->sub_species("accountant");

DESCRIPTION

Provides a very simple object for storing phylogenetic information. The classification is stored in an array, which is a list of nodes in a phylogenetic tree. Access to getting and setting species and genus is provided, but not to any of the other node types (eg: "phylum", "class", "order", "family"). There's plenty of scope for making the model more sophisticated, if this is ever needed.

A methods are also provided for storing common names, and subspecies.

CONTACT

James Gilbert email jgrg@sanger.ac.uk

APPENDIX

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

classification

 Title   : classification
 Usage   : $self->classification(@class_array);
           @classification = $self->classification();
 Function: Fills or returns the classification list in
           the object.  The array provided must be in
           the order SPECIES, GENUS ---> KINGDOM.
           Checks are made that species is in lower case,
           and all other elements are in title case.
 Example : $obj->classification(qw( sapiens Homo Hominidae
           Catarrhini Primates Eutheria Mammalia Vertebrata
           Chordata Metazoa Eukaryota));
 Returns : Classification array
 Args    : Classification array

common_name

 Title   : common_name
 Usage   : $self->common_name( $common_name );
           $common_name = $self->common_name();
 Function: Get or set the common name of the species
 Example : $self->common_name('human')
 Returns : The common name in a string
 Args    : String, which is the common name

 Title   : organelle
 Usage   : $self->organelle( $organelle );
           $organelle = $self->organelle();
 Function: Get or set the organelle name
 Example : $self->organelle('Chloroplast')
 Returns : The organelle name in a string
 Args    : String, which is the organelle name

species

 Title   : species
 Usage   : $self->species( $species );
           $species = $self->species();
 Function: Get or set the scientific species name.  The species
           name must be in lower case.
 Example : $self->species( 'sapiens' );
 Returns : Scientific species name as string
 Args    : Scientific species name as string

genus

 Title   : genus
 Usage   : $self->genus( $genus );
           $genus = $self->genus();
 Function: Get or set the scientific genus name.  The genus
           must be in title case.
 Example : $self->genus( 'Homo' );
 Returns : Scientific genus name as string
 Args    : Scientific genus name as string

sub_species

 Title   : sub_species
 Usage   : $obj->sub_species($newval)
 Function:
 Returns : value of sub_species
 Args    : newvalue (optional)

binomial

 Title   : binomial
 Usage   : $binomial = $self->binomial();
           $binomial = $self->binomial('FULL');
 Function: Returns a string "Genus species", or "Genus species subspecies",
           the first argument is 'FULL' (and the species has a subspecies).
 Args    : Optionally the string 'FULL' to get the full name including the
           the subspecies.

ncbi_taxid

 Title   : ncbi_taxid
 Usage   : $obj->ncbi_taxid($newval)
 Function:
 Returns : value of ncbi_taxid as string
 Args    : newvalue (optional)