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NCBITaxonomyTree.pm
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NCBITaxonomyTree.pm
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#!/usr/bin/perl
package NCBITaxonomyTree;
###
### Test using Bio::Taxon to look up taxonomy IDs by species name using the NCBI taxonomy dumps
###
### Brett Whitty
### whitty@msu.edu
###
use strict;
use warnings;
use Carp;
use Bio::Taxon;
use File::Basename qw{ dirname };
use Cwd qw{ abs_path };
my $no_cache = 0;
sub new {
my ($class, %args) = @_;
## argument 'no_cache' will prevent the object
## from caching the results of lookups for
## name_has_ancestor_name
## id_has_ancestor_name
## in case less memory usage is preferable to faster run time
if (defined($args{'no_cache'})) {
$no_cache = 1;
}
if (! defined($args{'path'})) {
## by default look for an NCBI taxonomy dump directory where the module is located
my $self_path = abs_path(dirname($INC{'NCBITaxonomyTree.pm'}));
my $dump_path = (-e "$self_path/taxonomy_dump") ? "$self_path/taxonomy_dump" : '';
if ($dump_path) {
$args{'path'} = $dump_path;
} else {
confess "Must provide path to NCBI taxonomy dump files with constructor 'path' argument";
}
}
_init_taxon_db($args{'path'});
return bless [], $class;
}
{
my $taxon_db;
my $cache = {};
sub get_children_species {
#my $pot = $taxon_db->get_taxon(-name => 'Solanum tuberosum');
#my @pot_c = $taxon_db->each_Descendent($pot);
## iterate through children and return array of species level tax ids
croak "Not implemented yet";
}
sub id_has_ancestor_name {
my ($self, $node_id, $name) = @_;
my $node = $taxon_db->get_taxon(-taxonid => $node_id) || confess "Taxon id '$node_id' not found in DB";
my $cache_key = "ihan|$node_id|$name";
return (defined($cache->{$cache_key})) ?
$cache->{$cache_key}
: _cache_result($cache_key, has_ancestor_name($self, $node, $name));
}
sub name_has_ancestor_name {
my ($self, $node_name, $name) = @_;
my $node = $taxon_db->get_taxon(-name => $node_name) || confess "Taxon name '$node_name' not found in DB";
my $cache_key = "nhan|$node_name|$name";
#use Data::Dumper;
#print Dumper $cache;
return (defined($cache->{$cache_key})) ?
$cache->{$cache_key}
: _cache_result($cache_key, has_ancestor_name($self, $node, $name));
}
sub has_ancestor_name {
## option for $node->rank cutoff?
my ($self, $node, $name) = @_;
my $ancestor = $taxon_db->get_taxon(-name => $name);
confess "Taxon name '$name' not found in DB" unless defined $ancestor;
_has_ancestor($node, $ancestor->id);
}
sub has_ancestor_id {
my ($self, $node, $id) = @_;
my $ancestor = $taxon_db->get_taxon(-taxonid => $id);
confess "Taxon id '$id' not found in DB" unless defined $ancestor;
_has_ancestor($node, $ancestor->id);
}
sub get_taxon_id {
my ($self, $name) = @_;
my $taxon = $taxon_db->get_taxon(-name => $name);
carp "Failed to find taxonomy node for '$name' in taxonomy db dump" unless defined $taxon;
return $taxon->id;
}
sub valid_scientific_name {
my ($self, $name) = @_;
if ($taxon_db->get_taxon(-name => $name)) {
return 1;
} else {
return 0;
}
}
sub get_scientific_name {
my ($self, $taxon_id) = @_;
my $taxon = $taxon_db->get_taxon(-taxonid => $taxon_id);
return $taxon->scientific_name;
}
sub get_common_name {
my ($self, $taxon_id) = @_;
my $taxon = $taxon_db->get_taxon(-taxonid => $taxon_id);
return $taxon->common_name;
}
sub is_valid_taxon_id {
my ($self, $taxon_id) = @_;
my $taxon = $taxon_db->get_taxon(-taxonid => $taxon_id);
return (defined($taxon)) ? 1 : 0;
}
sub get_taxon_id_for_rank_by_taxon_id {
my ($self, $node_id, $rank) = @_;
my $node = $taxon_db->get_taxon(-taxonid => $node_id) || confess "Taxon id '$node_id' not found in DB";
my $taxon_id = undef;
while ($node = $node->ancestor) {
if ($node->rank =~ /^$rank$/i) {
return $node->id;
}
}
return undef;
}
sub get_name_for_rank_by_taxon_id {
my ($self, $node_id, $rank) = @_;
my $taxon_id = $self->get_taxon_id_for_rank_by_taxon_id($node_id, $rank);
return $self->get_scientific_name($taxon_id);
}
sub _has_ancestor {
my ($node, $target_id) = @_;
my $ancestor = $node->ancestor || return 0;
if ($node->id eq $target_id) {
return 1;
} else {
_has_ancestor($node->ancestor, $target_id);
}
}
sub _init_taxon_db {
my ($path) = @_;
$taxon_db = new Bio::DB::Taxonomy(
-source => 'flatfile',
-directory => $path.'/index',
-nodesfile => $path.'/nodes.dmp',
-namesfile => $path.'/names.dmp',
);
return $taxon_db;
}
sub _cache_result {
my ($key, $result) = @_;
unless ($no_cache) {
$cache->{$key} = $result;
}
return $result;
}
}
1;