Bio::DB::Taxonomy - Access to a taxonomy database
use Bio::DB::Taxonomy; my $db = new Bio::DB::Taxonomy(-source => 'entrez'); # use NCBI Entrez over HTTP my $taxaid = $db->get_taxonid('Homo sapiens');
This is a front end module for access to a 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(-source => 'entrez'); Function: Builds a new Bio::DB::Taxonomy object Returns : an instance of Bio::DB::Taxonomy Args : -source => which database source 'entrez' or 'localfile'
Title : get_Taxonomy_Node Usage : my $species = $db->get_Taxonomy_Node(-taxonid => $taxaid) Function: Get a Bio::Taxonomy::Taxon object for a taxonid Returns : Bio::Taxonomy::Taxon object Args : -taxonid => taxonomy id (to query by taxonid) OR -name => string (to query by a taxonomy name: common name, species, genus, etc)
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 : String representing species/node name
Title : _load_tax_module Usage : *INTERNAL Bio::DB::Taxonomy stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
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.