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://redmine.open-bio.org/projects/bioperl/

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_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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq