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

NOTE: This class is planned for deprecation in favor of the simpler Bio::Taxon. Please use that class instead.

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.

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

James Gilbert email jgrg@sanger.ac.uk

CONTRIBUTORS

Sendu Bala, bix@sendu.me.uk Chris Fields, cjfields at bioperl dot org

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::Species->new(-classification => \@class)
 Function: Build a new Species object
 Returns : Bio::Species object
 Args    : -ncbi_taxid     => NCBI taxonomic ID (optional)
           -classification => arrayref of classification

classification

 Title   : classification
 Usage   : $self->classification(@class_array);
           @classification = $self->classification();
 Function: Get/set the lineage of this species. The array provided must be in
           the order ... ---> SPECIES, GENUS ---> KINGDOM ---> etc.
 Example : $obj->classification(qw( 'Homo sapiens' Homo Hominidae
           Catarrhini Primates Eutheria Mammalia Vertebrata
           Chordata Metazoa Eukaryota));
 Returns : Classification array
 Args    : Classification array 
                 OR
           A reference to the classification array. In the latter case
           if there is a second argument and it evaluates to true,
           names will not be validated. NB: in any case, names are never
           validated anyway.

ncbi_taxid

 Title   : ncbi_taxid
 Usage   : $obj->ncbi_taxid($newval)
 Function: Get/set the NCBI Taxon ID
 Returns : the NCBI Taxon ID as a string
 Args    : newvalue to set or undef to unset (optional)

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 (optional)

division

 Title   : division
 Usage   : $obj->division($newval)
 Function: Genbank Division for a species
 Returns : value of division (a scalar)
 Args    : value of division (a scalar)

species

 Title   : species
 Usage   : $self->species( $species );
           $species = $self->species();
 Function: Get or set the species name.
           Note that this is  NOT genus and species
           -- use $self->binomial() for that.
 Example : $self->species('sapiens');
 Returns : species name as string (NOT genus and species)
 Args    : species name as string (NOT genus and species)

genus

 Title   : genus
 Usage   : $self->genus( $genus );
           $genus = $self->genus();
 Function: Get or set the scientific genus name.
 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: Get or set the scientific subspecies name.
 Returns : value of sub_species
 Args    : newvalue (optional)

variant

 Title   : variant
 Usage   : $obj->variant($newval)
 Function: Get/set variant information for this species object (strain,
           isolate, etc).
 Example : 
 Returns : value of variant (a scalar)
 Args    : new value (a scalar or undef, optional)

binomial

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

validate_species_name

 Title   : validate_species_name
 Usage   : $result = $self->validate_species_name($string);
 Function: Validate the species portion of the binomial
 Args    : string
 Notes   : The string following the "genus name" in the NCBI binomial is so
           variable that it's not clear that this is a useful function. Consider
           the binomials "Simian 11 rotavirus (serotype 3 / strain
           SA11-Patton)", or "St. Thomas 3 rotavirus", straight from GenBank.
           This is particularly problematic in microbes and viruses. As such,
           this isn't actually used automatically by any Bio::Species method.

organelle

 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
 Note    : TODO: We currently do not know where the organelle definition will
           eventually go.  This is stored in the source seqfeature, though,
           so the information isn't lost.

Delegation

The following methods delegate to the internal Bio::Taxon instance. This is mainly to allow code continue using older methods, with the mind to migrate to using Bio::Taxon and related methods when this class is deprecated.

taxon

 Title    : taxon
 Usage    : $obj->taxon
 Function : retrieve the internal Bio::Taxon instance
 Returns  : A Bio::Taxon. If one is not previously set,
            an instance is created lazily
 Args     : Bio::Taxon (optional)

tree

 Title    : tree
 Usage    : $obj->tree
 Function : Returns a Bio::Tree::Tree object
 Returns  : A Bio::Tree::Tree. If one is not previously set,
            an instance is created lazily
 Args     : Bio::Tree::Tree (optional)