| Bio::DB::Taxonomy::entrez(3pm) | User Contributed Perl Documentation | Bio::DB::Taxonomy::entrez(3pm) |
Bio::DB::Taxonomy::entrez - Taxonomy Entrez driver
# 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.
A driver for querying NCBI Entrez Taxonomy database.
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.
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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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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)
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
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)
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)
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)
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
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'
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)
Title : authentication Usage : $db->authentication($user,$pass) Function: Get/Set authentication credentials Returns : Array of user/pass Args : Array or user/pass
| 2018-10-27 | perl v5.26.2 |