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Summary

Bio::DB::Taxonomy - Access to a taxonomy database

Package variables

Included modules

Inherit

Bio::Root::Root

Synopsis

  use Bio::DB::Taxonomy;
  my $db = Bio::DB::Taxonomy->new(-source => 'entrez');
  # use NCBI Entrez over HTTP
  my $taxonid = $db->get_taxonid('Homo sapiens');

  # get a taxon
  my $taxon = $db->get_taxon(-taxonid => $taxonid);

Description

This is a front end module for access to a taxonomy database.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::DB::Taxonomy->new(-source => 'entrez');
 Function: Builds a new Bio::DB::Taxonomy object.
 Returns : an instance of Bio::DB::Taxonomy
 Args    : -source => which database source 'entrez' (NCBI taxonomy online),
                      'flatfile' (local NCBI taxonomy), 'greengenes' (local
                      GreenGenes taxonomy), 'silva' (local Silva taxonomy), or
                      'list' (Do-It-Yourself taxonomy)

 Title   : get_num_taxa
 Usage   : my $num = $db->get_num_taxa();
 Function: Get the number of taxa stored in the database.
 Returns : A number
 Args    : None

 Title   : get_taxon
 Usage   : my $taxon = $db->get_taxon(-taxonid => $taxonid);
 Function: Get a Bio::Taxon object from the database.
 Returns : Bio::Taxon object
 Args    : just a single value which is the database id, OR named args:
           -taxonid => taxonomy id (to query by taxonid)
             OR
           -name    => string (to query by a taxonomy name: common name, 
                       scientific name, etc)

 Title   : get_taxonids
 Usage   : my @taxonids = $db->get_taxonids('Homo sapiens');
 Function: Searches for a taxonid (typically ncbi_taxon_id) based on a query
           string. Note that multiple taxonids can match to the same supplied
           name.
 Returns : array of integer ids in list context, one of these in scalar context
 Args    : string representing taxon's name

 Title   : get_tree
 Usage   : my $tree = $db->get_tree(@species_names);
 Function: Generate a tree comprised of the full lineages of all the supplied
           species names. The nodes for the requested species are given
           name('supplied') values corresponding to the supplied name, such that
           they can be identified if the real species name in the database
           (stored under node_name()) is different.
 Returns : Bio::Tree::Tree
 Args    : a list of species names (strings)

 Title   : ancestor
 Usage   : my $ancestor_taxon = $db->ancestor($taxon);
 Function: Retrieve the full ancestor taxon of a supplied Taxon from the
           database. 
 Returns : Bio::Taxon
 Args    : Bio::Taxon (that was retrieved from this database)

 Title   : each_Descendent
 Usage   : my @taxa = $db->each_Descendent($taxon);
 Function: Get all the descendents of the supplied Taxon (but not their
           descendents, ie. not a recursive fetchall).
 Returns : Array of Bio::Taxon objects
 Args    : Bio::Taxon (that was retrieved from this database)

 Title   : get_all_Descendents
 Usage   : my @taxa = $db->get_all_Descendents($taxon);
 Function: Like each_Descendent(), but do a recursive fetchall
 Returns : Array of Bio::Taxon objects
 Args    : Bio::Taxon (that was retrieved from this database)

 Title   : _load_tax_module
 Usage   : *INTERNAL Bio::DB::Taxonomy stuff*
 Function: Loads up (like use) a module at run time on demand

 Title   : _handle_internal_id
 Usage   : *INTERNAL Bio::DB::Taxonomy stuff*
 Function: Tries to ensure that when a taxon is requested from any database,
           the Taxon object returned will have the same internal id regardless
           of database.
 Args    : Bio::Taxon, and optionally true value to try and do the job using
           scientific name & rank if your ids aren't comparable to other dbs.

Methods code

sub new {

    my($class,@args) = @_;

    if( $class =~ /Bio::DB::Taxonomy::(\S+)/ ) {
        my ($self) = $class->SUPER::new(@args);
        $self->_initialize(@args);
        return $self;
    } else { 
        my %param = @args;
        @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
        my $source = $param{'-source'} || $DefaultSource;

        $source = "\L$source"; # normalize capitalization to lower case

        # normalize capitalization
        return unless( $class->_load_tax_module($source) );
        return "Bio::DB::Taxonomy::$source"->new(@args);
    }
}


# empty for now

}

sub get_num_taxa {

    shift->throw_not_implemented();

}

sub get_taxon {

    shift->throw_not_implemented();
}

*get_Taxonomy_Node =\& get_taxon;

}

sub get_taxonids {

    shift->throw_not_implemented();
}

*get_taxonid =\& get_taxonids;
*get_taxaid  =\& get_taxonids;

}

sub get_tree {

    my ($self, @species_names) = @_;
    
    # the full lineages of the species are merged into a single tree
    my $tree;
    foreach my $name (@species_names) {
        my $ncbi_id = $self->get_taxonid($name);
        if ($ncbi_id) {
            my $node = $self->get_taxon(-taxonid => $ncbi_id);
            $node->name('supplied', $name);
            
            if ($tree) {
                $tree->merge_lineage($node);
            }
            else {
                $tree = Bio::Tree::Tree->new(-verbose => $self->verbose, -node => $node);
            }
        }
        else {
            $self->throw("No taxonomy database node for species ".$name);
        }
    }
    
    return $tree;

}

sub ancestor {

    shift->throw_not_implemented();

}

sub each_Descendent {

    shift->throw_not_implemented();

}

sub get_all_Descendents {

    my ($self, $taxon) = @_;
    my @taxa;
    foreach my $desc_taxon ($self->each_Descendent($taxon)) {
        push @taxa, ($desc_taxon, $self->get_all_Descendents($desc_taxon));
    }
    return @taxa;

}

sub _load_tax_module {

    my ($self, $source) = @_;
    my $module = "Bio::DB::Taxonomy::" . $source;
    my $ok;

    eval { $ok = $self->_load_module($module) };
    if ( $@ ) {
        print STDERR $@;
        print STDERR <<END;
$self: $source cannot be found
Exception $@
For more information about the Bio::DB::Taxonomy system please see
the Bio::DB::Taxonomy docs.  This includes ways of checking for 
formats at compile time, not run time.
END
  ;
    }
    return $ok;

}

sub _handle_internal_id {

    my ($self, $taxon, $try_name) = @_;
    $self->throw("Must supply a Bio::Taxon") unless ref($taxon) && $taxon->isa('Bio::Taxon');
    my $taxid = $taxon->id || return;
    my $sci_name = $taxon->scientific_name || '';
    my $rank = $taxon->rank || 'no rank';
    
    if ($try_name && $sci_name && defined $TAXON_IIDS->{names}->{$sci_name}) {
        if (defined $TAXON_IIDS->{names}->{$sci_name}->{$rank}) {
            $TAXON_IIDS->{taxids}->{$taxid} = $TAXON_IIDS->{names}->{$sci_name}->{$rank};
        }
        elsif ($rank eq 'no rank') {
            # pick the internal id of one named rank taxa at random
            my ($iid) = values %{$TAXON_IIDS->{names}->{$sci_name}};
            $TAXON_IIDS->{taxids}->{$taxid} = $iid;
        }
    }
    
    if (defined $TAXON_IIDS->{taxids}->{$taxid}) {
        # a little dangerous to use this internal method of Bio::Tree::Node;
        # but it is how internal_id() is set
        $taxon->_creation_id($TAXON_IIDS->{taxids}->{$taxid});
    }
    else {
        $TAXON_IIDS->{taxids}->{$taxid} = $taxon->internal_id;
        $TAXON_IIDS->{names}->{$sci_name}->{$rank} = $taxon->internal_id if $sci_name;
    }
}


1;

}

General documentation

User feedback is an integral part of the evolution of this and other
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with code and data examples if at all possible.

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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _