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 = new Bio::DB::Taxonomy(-source => 'entrez'); my $taxaid = $db->get_taxaid('Homo sapiens');
A driver for querying NCBI Entrez Taxonomy database.
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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 = 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
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.
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
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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.