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 listsSupport
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/issuesAUTHOR - 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
defaultget_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 : Noneget_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 nameancestor
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 HashrefBio::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