Summary

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

Package variables

Included modules

Inherit

Bio::Root::HTTPget

Synopsis

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

Description

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

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::DB::Taxonomy(-source => 'entrez');
 Function: Builds a new Bio::DB::Taxonomy object 
 Returns : an instance of Bio::DB::Taxonomy
 Args    : -source => which database source 'entrez' or 'localfile'

 Title   : get_Taxonomy_Node
 Usage   : my $species = $db->get_Taxonomy_Node(-taxonid => $taxaid)
 Function: Get a Bio::Taxonomy::Taxon object for a taxonid
 Returns : Bio::Taxonomy::Taxon object
 Args    : -taxonid => taxonomy id (to query by taxonid)
            OR
           -name   => string (to query by a taxonomy name: common name, 
                              species, genus, etc)

 Title   : get_taxonid
 Usage   : my $taxonid = $db->get_taxonid('Homo sapiens');
 Function: Searches for a taxonid (typically ncbi_taxon_id) 
           based on a query string 
 Returns : Integer ID
 Args    : String representing species/node name

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

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

}

sub _initialize {

}

sub get_Taxonomy_Node {

   my ($self) = @_;

    $self->throw_not_implemented();

}

sub get_taxonid {

   my ($self) = @_;

    $self->throw_not_implemented();

}

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;

}

General documentation

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.

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of the bugs and their resolution. Bug reports can be submitted via
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  http://bugzilla.bioperl.org/

Email jason-at-bioperl.org
Describe contact details here

Additional contributors names and emails here

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