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Bio::DB::Taxonomy::flaUsereContributed Perl DocuBio::DB::Taxonomy::flatfile(3)

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
	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)

perl v5.32.0			  2019-12-07	Bio::DB::Taxonomy::flatfile(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

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