Raw content of Bio::EnsEMBL::Compara::NCBITaxon
<![CDATA[=head1 NAME
NCBITaxon - DESCRIPTION of Object
=head1 DESCRIPTION
An object that hold a node within a taxonomic tree. Inherits from NestedSet.
From Bio::Species
classification
common_name
binomial
Here are also the additional methods in Bio::Species that "might" be useful, but let us
forget about these for now.
genus
species
sub_species
variant
organelle
division
=head1 CONTACT
Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::NCBITaxon;
use strict;
use Bio::Species;
use Bio::EnsEMBL::Compara::NestedSet;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Utils::Argument;
our @ISA = qw(Bio::EnsEMBL::Compara::NestedSet);
=head2 copy
Arg [1] : int $member_id (optional)
Example :
Description: returns copy of object, calling superclass copy method
Returntype :
Exceptions :
Caller :
=cut
sub copy {
my $self = shift;
my $mycopy = $self->SUPER::copy;
bless $mycopy, "Bio::EnsEMBL::Compara::NCBITaxon";
$mycopy->ncbi_taxid($self->ncbi_taxid);
$mycopy->rank($self->rank);
$mycopy->genbank_hidden_flag($self->genbank_hidden_flag);
return $mycopy;
}
sub ncbi_taxid {
my $self = shift;
my $value = shift;
$self->node_id($value) if($value);
return $self->node_id;
}
sub taxon_id {
my $self = shift;
my $value = shift;
$self->node_id($value) if($value);
return $self->node_id;
}
sub dbID {
my $self = shift;
my $value = shift;
$self->node_id($value) if($value);
return $self->node_id;
}
sub rank {
my $self = shift;
$self->{'_rank'} = shift if(@_);
return $self->{'_rank'};
}
sub genbank_hidden_flag {
my $self = shift;
$self->{'_genbank_hidden_flag'} = shift if(@_);
return $self->{'_genbank_hidden_flag'};
}
sub classification {
my $self =shift;
my @args = @_;
my ($separator, $full);
if (scalar @args) {
($separator, $full) = rearrange([qw(SEPARATOR FULL)], @args);
}
$separator = " " unless(defined $separator);
$full = 0 unless (defined $full);
$self->{"_separator"} = $separator unless (defined $self->{"_separator"});
$self->{"_separator_full"} = $separator unless (defined $self->{"_separator_full"});
$self->{'_classification'} = undef unless ($self->{"_separator"} eq $separator);
$self->{'_classification_full'} = undef unless ($self->{"_separator_full"} eq $separator);
return $self->{'_classification_full'} if ($full && defined $self->{'_classification_full'});
return $self->{'_classification'} if (!$full && defined $self->{'_classification'});
my $root = $self->root;
my @classification;
unless ($root->name eq "root") {
unshift @classification, $self->name;
}
unless ($root->get_child_count == 0) {
$root->_add_child_name_to_classification(\@classification, $full);
}
if ($self->rank eq 'species' || $self->rank eq 'subspecies') {
my ($genus, $species, $subspecies) = split(" ", $self->binomial);
unshift @classification, $species;
unshift @classification, $subspecies if (defined $subspecies);
}
if ($full) {
$self->{'_classification_full'} = join($separator,@classification);
$self->{"_separator_full"} = $separator;
return $self->{'_classification_full'};
} else {
$self->{'_classification'} = join($separator,@classification);
$self->{"_separator"} = $separator;
return $self->{'_classification'};
}
}
=head2 subspecies
Example : $ncbi->subspecies;
Description: Returns the subspeceis name for this species
Example : "verus" for Pan troglodytes verus
Returntype : string
Exceptions :
Caller : general
=cut
sub subspecies {
my $self = shift;
unless (defined $self->{'_species'}) {
my ($genus, $species, $subspecies) = split(" ", $self->binomial);
$self->{'_species'} = $species;
$self->{'_genus'} = $genus;
$self->{'_subspecies'} = $subspecies;
}
return $self->{'_species'};
}
=head2 species
Example : $ncbi->species;
Description: Returns the speceis name for this species
Example : "sapiens" for Homo sapiens
Returntype : string
Exceptions :
Caller : general
=cut
sub species {
my $self = shift;
unless (defined $self->{'_species'}) {
my ($genus, $species, $subspecies) = split(" ", $self->binomial);
$self->{'_species'} = $species;
$self->{'_genus'} = $genus;
$self->{'_subspecies'} = $subspecies;
}
return $self->{'_species'};
}
=head2 genus
Example : $ncbi->genus;
Description: Returns the genus name for this species
Returntype : string
Example : "Homo" for Homo sapiens
Exceptions :
Caller : general
=cut
sub genus {
my $self = shift;
unless (defined $self->{'_genus'}) {
my ($genus, $species, $subspecies) = split(" ", $self->binomial);
$self->{'_species'} = $species;
$self->{'_genus'} = $genus;
$self->{'_subspecies'} = $subspecies;
}
return $self->{'_genus'};
}
sub _add_child_name_to_classification {
my $self = shift;
my $classification = shift;
my $full = shift;
if ($self->get_child_count > 1) {
throw("Can't classification on a multifurcating tree\n");
} elsif ($self->get_child_count == 1) {
my $child = $self->children->[0];
if ($full) {
unshift @$classification, $child->name unless ($child->rank eq "subgenus"
|| $child->rank eq "subspecies"
|| $child->rank eq "species");
} else {
unless ($child->genbank_hidden_flag || $child->rank eq "subgenus") {
unshift @$classification, $child->name;
}
}
unless ($child->rank eq 'species') {
$child->_add_child_name_to_classification($classification, $full);
}
}
}
=head2 common_name
Example : $ncbi->common_name;
Description: The comon name as defined by Genbank
Returntype : string
Exceptions : returns undef if no genbank common name exists.
Caller : general
=cut
sub common_name {
my $self = shift;
if ($self->has_tag('genbank common name') && $self->rank eq 'species') {
return $self->get_tagvalue('genbank common name');
} else {
return undef;
}
}
=head2 ensembl_alias_name
Example : $ncbi->ensembl_alias_name;
Description: The comon name as defined by ensembl alias
Returntype : string
Exceptions : returns undef if no ensembl alias name exists.
Caller : general
=cut
sub ensembl_alias_name {
my $self = shift;
#Not checking for rank as we do above, because we do not get dog since the
#rank for dog is subspecies (ensembl-51).
if ($self->has_tag('ensembl alias name')) {
return $self->get_tagvalue('ensembl alias name');
} else {
return undef;
}
}
=head2 binomial
Example : $ncbi->binomial;
Description: The binomial name (AKA the scientific name) of this genome
Returntype : string
Exceptions : warns when node is not a species or has no scientific name
Caller : general
=cut
sub binomial {
my $self = shift;
if ($self->has_tag('scientific name') && ($self->rank eq 'species' || $self->rank eq 'subspecies')) {
return $self->get_tagvalue('scientific name');
} else {
warning("taxon_id=",$self->node_id," is not a species or subspecies. So binomial is undef\n");
return undef;
}
}
=head2 ensembl_alias
Example : $ncbi->ensembl_alias;
Description: The ensembl_alias name (AKA the name in the ensembl website) of this genome
Returntype : string
Exceptions : warns when node is not a species or has no ensembl_alias
Caller : general
=cut
sub ensembl_alias {
my $self = shift;
if ($self->has_tag('ensembl alias name')) {
return $self->get_tagvalue('ensembl alias name');
} else {
warning("taxon_id=",$self->node_id," is not a species or subspecies. So ensembl_alias is undef\n");
return undef;
}
}
=head2 short_name
Example : $ncbi->short_name;
Description: The name of this genome in the Gspe ('G'enera
'spe'cies) format.
Returntype : string
Exceptions : none
Caller : general
=cut
sub short_name {
my $self = shift;
my $name = $self->name;
$name =~ s/(\S)\S+\s(\S{3})\S+/$1$2/;
$name =~ s/\ //g;
return $name;
}
sub get_short_name {
my $self = shift;
return $self->short_name;
}
sub RAP_species_format {
my $self = shift;
my $newick = "";
if($self->get_child_count() > 0) {
$newick .= "(";
my $first_child=1;
foreach my $child (@{$self->sorted_children}) {
$newick .= "," unless($first_child);
$newick .= $child->newick_format;
$first_child = 0;
}
$newick .= ")";
}
$newick .= sprintf("\"%s\"", $self->name,);
$newick .= sprintf(":%1.4f", $self->distance_to_parent) if($self->distance_to_parent > 0);
if(!($self->has_parent)) {
$newick .= ";";
}
return $newick;
}
sub print_node {
my $self = shift;
printf("(%s", $self->node_id);
printf(" %s", $self->rank) if($self->rank);
print(")");
printf("%s", $self->name) if($self->name);
print("\n");
}
1;
]]>