NAME

Bio::Taxonomy::Node - A node in a represented taxonomy

SYNOPSIS

  use Bio::Taxonomy::Node;
  # typically you will get a Node from a Bio::DB::Taxonomy object
  # but here is how you initialize one
  my $node = new Bio::Taxonomy::Node(-name      => $name,
                                     -object_id => $oid,
                                     -parent_id => $pid,
                                     -rank   => $rank,
                                     -division  => $div,
                                     -dbh       => $dbh);

  my $dbh = new Bio::DB::Taxonomy(-source   => 'flatfile',
                                  -directory=> '/tmp',
                                  -nodesfile=> '/path/to/nodes.dmp',
                                  -namesfile=> '/path/to/names.dmp');
  my $hum_node = $dbh->get_Taxonomy_Node(-name => 'Homo sapiens');
  my $hum_node2= $dbh->get_Taxonomy_Node(-taxonid => '9606');

  print "rank is ", $hum_node->rank, "\n";
  print "classification is ", join(" ", $hum_node->classification),"\n"; 
  print "division is ", $node->division, "\n";

DESCRIPTION

This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called Bio::Species. This new implementation allows representation of the intermediete nodes not just the species nodes and can relate their connections.

FEEDBACK

Mailing Lists

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.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

Describe contact details here

CONTRIBUTORS

Juguang Xiao, juguang@tll.org.sg

Additional contributors names and emails here

APPENDIX

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

new

 Title   : new
 Usage   : my $obj = new Bio::Taxonomy::Node();
 Function: Builds a new Bio::Taxonomy::Node object 
 Returns : an instance of Bio::Taxonomy::Node
 Args    : -dbh       => a reference to a Bio::DB::Taxonomy object
           -name      => a string representing the node name
           -object_id => unique identifier - typically NCBI Taxid

db_handle

 Title   : db_handle
 Usage   : $obj->db_handle($newval)
 Function: Get/Set Bio::DB::Taxonomy Handle
 Returns : value of db_handle (a scalar) (Bio::DB::Taxonomy object)
 Args    : on set, new value (a scalar or undef, optional) Bio::DB::Taxonomy object

factory

  Title:    factory
  Usage:    $factory->factory($newval);
  Function: Get/Set Bio::Taxonomy::FactoryI implementation
  Returns:  Bio:;Taxonomy::FactoryI
  Args:     Bio::Taxonomy::FactoryI

rank

 Title   : rank
 Usage   : $obj->rank($newval)
 Function: 
 Example : 
 Returns : value of rank (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

object_id

 Title   : object_id
 Usage   : $obj->object_id($newval)
 Function: 
 Example : 
 Returns : value of object_id (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

version

 Title   : version
 Usage   : $obj->version($newval)
 Function: 
 Example : 
 Returns : value of version (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

authority

 Title   : authority
 Usage   : $obj->authority($newval)
 Function: 
 Example : 
 Returns : value of authority (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

namespace

 Title   : namespace
 Usage   : $obj->namespace($newval)
 Function: 
 Example : 
 Returns : value of namespace (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

parent_id

 Title   : parent_id
 Usage   : $obj->parent_id($newval)
 Function: 
 Example : 
 Returns : value of parent_id (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

get_Parent_Node

 Title   : get_Parent_Node
 Usage   : my $parentnode = $node->get_Parent_Node()
 Function: Retrieve the full Parent node from the database
 Returns : Bio::Taxonomy::Node
 Args    : none

node_name

 Title   : node_name
 Usage   : $obj->node_name($newval)
 Function: 
 Example : 
 Returns : value of node_name (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

classification

 Title   : classification
 Usage   : $self->classification(@class_array);
           @classification = $self->classification();
 Function: Fills 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.
 Returns : Classification array
 Args    : none - this can be set directly

division

 Title   : division
 Usage   : $obj->division($newval)
 Function: 
 Example : 
 Returns : value of division (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

show_all

 Title   : show_all
 Usage   : $obj->show_all($newval)
 Function: Boolean flag whether or not we should show all intermediete
           nodes that do not have actual ranks.
 Returns : value of show_all (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

name

  Title:    name
  Usage:    $obj->name('scientific', 'sapiens');
            $obj->name('common', 'human', 'man');
            my @names = @{$obj->name('common')};
  Function: Get and set the names
  Returns:  names (a array reference)
  Args:     Arg1 => the name_class. You can assign any text, but the words
                'scientific' and 'common' have the special meaning, as
                scientific name and common name, respectively.
            Arg2 .. => the names

scientific_name

  Title:    scientific_name
  Usage:    my $new_val = $obj->scientific_name($newval);
  Function: Get/Set the scientific name
  Returns:  a scalar text value
  Args:     a scalar text value

parent_taxon_id

  Title   : parent_taxon_id
  Usage   : $self->parent_taxon_id($newval);
            $val = $self->parent_taxon_id;
  Function: Get/Set for parent_taxon_id
  Return  : 
  Args    :    

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq