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
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Reporting Bugs
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AUTHOR - Jason Stajich
Email jason-at-bioperl.orgCONTRIBUTORS
Sendu Bala: [email protected]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