Bio::DB::Taxonomy::list - An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
use Bio::DB::Taxonomy; my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens'); my @ranks = qw(superkingdom class genus species); my $db = Bio::DB::Taxonomy->new(-source => 'list', -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 : $db->add_lineage(-names => \@names) 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 : n/a Args : -names => [] : array ref of scientific names, REQUIRED -ranks => [] : array ref of rank names, same order as above, OPTIONAL
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; 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)
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)
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.