Bio
Species
Summary
Bio::Species - Generic species object
Package variables
No package variables defined.
Included modules
Inherit
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.
Methods
Methods description
Title : classification
Usage : $self->classification(@class_array);
@classification = $self->classification();
Function: Fills or returns the classification list in
the object. The array provided must be in
the order SPECIES, GENUS ---> KINGDOM.
Checks are made that species is in lower case,
and all other elements are in title case.
Example : $obj->classification(qw( sapiens Homo Hominidae
Catarrhini Primates Eutheria Mammalia Vertebrata
Chordata Metazoa Eukaryota));
Returns : Classification array
Args : Classification array |
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 |
Title : species
Usage : $self->species( $species );
$species = $self->species();
Function: Get or set the scientific species name. The species
name must be in lower case.
Example : $self->species( 'sapiens' );
Returns : Scientific species name as string
Args : Scientific species name as string |
Title : genus
Usage : $self->genus( $genus );
$genus = $self->genus();
Function: Get or set the scientific genus name. The genus
must be in title case.
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:
Returns : value of sub_species
Args : newvalue (optional) |
Title : binomial
Usage : $binomial = $self->binomial();
$binomial = $self->binomial('FULL');
Function: Returns a string "Genus species", or "Genus species subspecies",
the first argument is 'FULL' (and the species has a subspecies).
Args : Optionally the string 'FULL' to get the full name including the
the subspecies. |
Title : ncbi_taxid
Usage : $obj->ncbi_taxid($newval)
Function:
Returns : value of ncbi_taxid as string
Args : newvalue (optional) |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'classification'} = [];
$self->{'common_name'} = undef;
my ($classification) = $self->_rearrange([qw(CLASSIFICATION)], @args);
if( defined $classification &&
(ref($classification) =~ /array/i) ) {
$self->classification(@$classification);
}
return $self;} | sub classification
{ my ($self,@args) = @_;
if (@args) {
{
my $species = $args[0];
$self->validate_species_name( $species );
for (my $i = 1; $i < @args; $i++) {
$self->validate_name( $args[$i] );
}
}
$self->{'classification'} = [ @args ];
}
return @{$self->{'classification'}};} | sub common_name
{ my($self, $name) = @_;
if ($name) {
$self->{'common_name'} = $name;
} else {
return $self->{'common_name'}
}} | sub organelle
{ my($self, $name) = @_;
if ($name) {
$self->{'organelle'} = $name;
} else {
return $self->{'organelle'}
}} | sub species
{ my($self, $species) = @_;
if ($species) {
$self->validate_species_name( $species );
$self->{'classification'}[0] = $species;
}
return $self->{'classification'}[0];} | sub genus
{ my($self, $genus) = @_;
if ($genus) {
$self->validate_name( $genus );
$self->{'classification'}[1] = $genus;
}
return $self->{'classification'}[1];} | sub sub_species
{ my( $self, $sub ) = @_;
if ($sub) {
$self->{'_sub_species'} = $sub;
}
return $self->{'_sub_species'};} | sub binomial
{ my( $self, $full ) = @_;
my( $species, $genus ) = $self->classification();
unless( defined $species) {
$species = '';
$self->warn("classification was not set");
}
$genus = '' unless( defined $genus);
my $bi = "$genus $species";
if (defined($full) && ($full eq 'FULL')) {
my $ssp = $self->sub_species;
$bi .= " $ssp" if $ssp;
}
return $bi;} | sub validate_species_name
{ my( $self, $string ) = @_;
$string =~ /^[\S\d\.]+$||""/ or
$self->throw("Invalid species name '$string'");} | sub validate_name
{ my( $self, $string ) = @_;
return $string =~ /^[A-Z][a-z]+$/ or
$self->throw("Invalid name '$string' (Wrong case?)");} | sub ncbi_taxid
{ my( $self, $sub ) = @_;
if ($sub) {
$self->{'_ncbi_taxid'} = $sub;
}
return $self->{'_ncbi_taxid'};} | General documentation
James Gilbert email jgrg@sanger.ac.uk
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
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