NAME

Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver

SYNOPSIS

# Do not use this object directly, rather through the Bio::DB::Taxonomy # interface

  use Bio::DB::Taxonomy;

  my $db = Bio::DB::Taxonomy->new(-source => 'entrez');

  my $taxonid = $db->get_taxonid('Homo sapiens');
  my $node   = $db->get_Taxonomy_Node(-taxonid => $taxonid);

  my $gi = 71836523;
  my $node = $db->get_Taxonomy_Node(-gi => $gi, -db => 'protein');
  print $node->binomial, "\n";
  my ($species,$genus,$family) =  $node->classification;
  print "family is $family\n";

  # Can also go up 4 levels
  my $p = $node;
  for ( 1..4 ) {
    $p = $db->get_Taxonomy_Node(-taxonid => $p->parent_id);
  }
  print $p->rank, " ", ($p->classification)[0], "\n";

  # could then classify a set of BLAST hits based on their GI numbers
  # into taxonomic categories.

It is not currently possibly to query a node for its children so we cannot completely replace the advantage of the flatfile Bio::DB::Taxonomy::flatfile module.

DESCRIPTION

A driver for querying NCBI Entrez Taxonomy database.

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/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

CONTRIBUTORS

Sendu Bala: bix@sendu.me.uk

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 = Bio::DB::Taxonomy::entrez->new();
 Function: Builds a new Bio::DB::Taxonomy::entrez object
 Returns : an instance of Bio::DB::Taxonomy::entrez
 Args    : -location => URL to Entrez (if you want to override the default)
           -params   => Hashref of URL params if you want to override the
                        default

get_num_taxa

 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

get_taxon

 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)
            OR
           To retrieve a taxonomy node for a GI number provide the -gi option
           with the gi number and -db with either 'nucleotide' or 'protein' to
           define the db.
            AND optionally,
           -full    => 1 (to force retrieval of full information - sometimes
                          minimal information about your taxon may have been
                          cached, which is normally used to save database
                          accesses)

get_taxonids

 Title   : get_taxonids
 Usage   : my $taxonid = $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

ancestor

 Title   : ancestor
 Usage   : my $ancestor_taxon = $db->ancestor($taxon)
 Function: Retrieve the ancestor taxon of a supplied Taxon from the database.

           Note that unless the ancestor has previously been directly
           requested with get_taxon(), the returned Taxon object will only have
           a minimal amount of information.

 Returns : Bio::Taxon
 Args    : Bio::Taxon (that was retrieved from this database)

each_Descendent

 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).

           Note that this implementation is unable to return a taxon that
           hasn't previously been directly fetched with get_taxon(), or wasn't
           an ancestor of such a fetch.

 Returns : Array of Bio::Taxon objects
 Args    : Bio::Taxon (that was retrieved from this database)

Some Get/Setter methods

entrez_url

 Title   : entrez_url
 Usage   : $obj->entrez_url($newval)
 Function: Get/set entrez URL
 Returns : value of entrez url (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

entrez_params

 Title   : entrez_params
 Usage   : $obj->entrez_params($newval)
 Function: Get/set entrez params
 Returns : value of entrez_params (a hashref)
 Args    : on set, new value Hashref

Bio::DB::WebBase methods

proxy_string

 Title   : proxy_string
 Usage   : my $proxy_string = $self->proxy_string($protocol)
 Function: Get the proxy string (plus user/pass )
 Returns : string
 Args    : protocol ('http' or 'ftp'), default 'http'

proxy

 Title   : proxy
 Usage   : $httpproxy = $db->proxy('http')  or
           $db->proxy(['http','ftp'], 'http://myproxy' )
 Function: Get/Set a proxy for use of proxy
 Returns : a string indicating the proxy
 Args    : $protocol : an array ref of the protocol(s) to set/get
           $proxyurl : url of the proxy to use for the specified protocol
           $username : username (if proxy requires authentication)
           $password : password (if proxy requires authentication)

authentication

 Title   : authentication
 Usage   : $db->authentication($user,$pass)
 Function: Get/Set authentication credentials
 Returns : Array of user/pass
 Args    : Array or user/pass