Bio::Species(3)

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.

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:

  http://bugzilla.open-bio.org/

AUTHOR
James Gilbert email jgrg@sanger.ac.uk

CONTRIBUTORS
Sendu Bala, bix@sendu.me.uk

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 scientific species name.
 Example : $self->species('Homo 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.
 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.

  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