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BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Species

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://redmine.open-bio.org/projects/bioperl/

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)