Bio::DB::Taxonomy::list - An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new( -source => 'list' ); my @ranks = ('superkingdom', 'class', 'genus', 'species'); my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens'); $db->add_lineage(-names => \@names, -ranks => \@ranks); @names = ('Eukaryota', 'Mammalia', 'Mus', 'Mus musculus'); $db->add_lineage(-names => \@names, -ranks => \@ranks);
This is an implementation which uses supplied lists of words to create a database from which you can extract Bio::Taxon objects.
It is possible this module could do something like store the data it builds up to disc. Would that be useful? At any rate, this is why the module is called 'list' and not 'in_memory' or similar.
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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::list->new(); Function: Builds a new Bio::DB::Taxonomy::list object Returns : an instance of Bio::DB::Taxonomy::list Args : optional, as per the add_lineage() method.
Title : add_lineage Usage : my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens'); my @ranks = ('superkingdom', 'class', 'genus', 'species'); $db->add_lineage( -names => \@names, -ranks => \@ranks ); Function: Add a lineage to the database, where the lineage is described by a list of scientific names in the order root->leaf. The rank of each name can optionally be described by supplying an additional list of rank names in the same order (eg. superkingdom->species). Returns : 1 for success Args : -names =>  : array ref of scientific names, REQUIRED -ranks =>  : array ref of rank names, same order as above, OPTIONAL
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 : A single value which is the ID of the taxon to retrieve OR named args, as follows: -taxonid => Taxonomy ID (NB: these are not NCBI taxonomy ids but 'list' pre-fixed ids unique to the list database). OR -name => String (to query by a taxonomy name). A given taxon name can match different taxonomy objects. When that is the case, a warning is displayed and the first matching taxon is reported. See get_taxonids() to get all matching taxon IDs. OR -names => Array ref of lineage names, like in add_lineage(). To overcome the limitations of -name, you can use -names to provide the full lineage of the taxon you want and get a unique, unambiguous taxon object.
Title : get_taxonids Usage : my @taxonids = $db->get_taxonids('Homo sapiens'); Function: Searches for a taxonid (generated by the list module) 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 full ancestor taxon of a supplied Taxon from the database. 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). Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database)