Bio::Species - Generic species object.
$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");
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.
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
James Gilbert email email@example.com
Sendu Bala, firstname.lastname@example.org Chris Fields, cjfields at bioperl dot org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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.
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)
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)
Title : division Usage : $obj->division($newval) Function: Genbank Division for a species Returns : value of division (a scalar) Args : value of division (a scalar)
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)
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
Title : sub_species Usage : $obj->sub_species($newval) Function: Get or set the scientific subspecies name. Returns : value of sub_species Args : newvalue (optional)
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)
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
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.
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.
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.
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)
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)