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Bio::Species.3pm
Langue: en
Version: 2010-05-19 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Species - Generic species objectSYNOPSIS
$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.ukCONTRIBUTORS
Sendu Bala, bix@sendu.me.ukAPPENDIX
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
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre