/ 
bioperl-1.4
/ Bio::DB::Taxonomy::entrez

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

my $taxaid = $db->get_taxaid('Homo sapiens');

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/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.org

CONTRIBUTORS

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::DB::Taxonomy::entrez();
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_Taxonomy_Node

Title   : get_Taxonomy_Node
Usage   : my $species = $db->get_Taxonomy_Node(-taxonid => $taxonid)
Function: Get a Bio::Taxonomy::Taxon object
Returns : Bio::Taxonomy::Taxon object(s) [more than one
Args    : -taxonid => taxonomy id (to query by taxonid)
           OR
          -name   => string (to query by a taxonomy name: common name,
                             species, genus, etc)
          or just a single value which is the taxid.

get_taxonid

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    : Array of Strings representing species/node name

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