NAME¶
Bio::DB::Taxonomy::flatfile - Use the NCBI taxonomy from local indexed flat
files
SYNOPSIS¶
use Bio::DB::Taxonomy;
my $db = Bio::DB::Taxonomy->new(-source => 'flatfile' ,
-nodesfile => 'nodes.dmp',
-namesfile => 'names.dmp');
DESCRIPTION¶
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
FEEDBACK¶
Mailing Lists¶
User feedback is an integral part of the evolution of this and other Bioperl
modules. Send your comments and suggestions preferably to the Bioperl mailing
list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support¶
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive
experts will be able look at the problem and quickly address it. Please
include a thorough description of the problem with code and data examples if
at all possible.
Reporting Bugs¶
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs
and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Jason Stajich¶
Email jason-at-bioperl-dot-org
CONTRIBUTORS¶
Sendu Bala: bix@sendu.me.uk
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
new¶
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
Bio::DB::Taxonomy interface implementation¶
get_num_taxa¶
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
get_taxon¶
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)
get_taxonids¶
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
get_Children_Taxids¶
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())
ancestor¶
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)
each_Descendent¶
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)
Helper methods¶
index_directory¶
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)