Bio::Species man page on Pidora

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Bio::Species(3)	      User Contributed Perl Documentation      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

perl v5.14.1			  2011-07-22		       Bio::Species(3)
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