Bio::Species.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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