| Bio::DB::Taxonomy::flatfile(3pm) | User Contributed Perl Documentation | Bio::DB::Taxonomy::flatfile(3pm) |
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
Function : 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)
| 2021-08-15 | perl v5.32.1 |