Bio::DB::Taxonomy::flatfile - Use the NCBI taxonomy from local indexed flat files
use Bio::DB::Taxonomy; my $db = Bio::DB::Taxonomy->new(-source => 'flatfile' , -nodesfile => 'nodes.dmp', -namesfile => 'names.dmp');
This is an implementation of Bio::DB::Taxonomy which stores and accesses the NCBI taxonomy using flat files stored locally on disk and indexed using the DB_File module RECNO data structure for fast retrieval.
The required database files, nodes.dmp and names.dmp can be obtained from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
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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::flatfile->new(); Function: Builds a new Bio::DB::Taxonomy::flatfile object Returns : an instance of Bio::DB::Taxonomy::flatfile Args : -directory => name of directory where index files should be created -nodesfile => name of file containing nodes (nodes.dmp from NCBI) -namesfile => name of the file containing names(names.dmp from NCBI) -force => 1 to replace current indexes even if they exist
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 : 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)
Title : get_taxonids Usage : my @taxonids = $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
Title : get_Children_Taxids Usage : my @childrenids = $db->get_Children_Taxids Function: Get the ids of the children of a node in the taxonomy Returns : Array of Ids Args : Bio::Taxon or a taxon_id Status : deprecated (use each_Descendent())
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)
Title : index_directory Funtion : Get/set the location that index files are stored. (this module will index the supplied database) Usage : $obj->index_directory($newval) Returns : value of index_directory (a scalar) Args : on set, new value (a scalar or undef, optional)