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Bio::DB::Taxonomy.3pm
Langue: en
Version: 2008-06-24 (ubuntu - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::DB::Taxonomy - Access to a taxonomy databaseSYNOPSIS
use Bio::DB::Taxonomy; my $db = new Bio::DB::Taxonomy(-source => 'entrez'); # use NCBI Entrez over HTTP my $taxonid = $db->get_taxonid('Homo sapiens'); # get a taxon my $taxon = $db->get_taxon(-taxonid => $taxonid);
DESCRIPTION
This is a front end module for access to a taxonomy database.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
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:
http://bugzilla.open-bio.org/
AUTHOR - Jason Stajich
Email jason-at-bioperl.orgCONTRIBUTORS
Sendu Bala: bix@sendu.me.ukAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new Usage : my $obj = new Bio::DB::Taxonomy(-source => 'entrez'); Function: Builds a new Bio::DB::Taxonomy object. Returns : an instance of Bio::DB::Taxonomy Args : -source => which database source 'entrez' or 'flatfile' or 'list'
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
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)
get_all_Descendents
Title : get_all_Descendents Usage : my @taxa = $db->get_all_Descendents($taxon); Function: Like each_Descendent(), but do a recursive fetchall Returns : Array of Bio::Taxon objects Args : Bio::Taxon (that was retrieved from this database)
_load_tax_module
Title : _load_tax_module Usage : *INTERNAL Bio::DB::Taxonomy stuff* Function: Loads up (like use) a module at run time on demand
_handle_internal_id
Title : _handle_internal_id Usage : *INTERNAL Bio::DB::Taxonomy stuff* Function: Tries to ensure that when a taxon is requested from any database, the Taxon object returned will have the same internal id regardless of database. Args : Bio::Taxon, and optionally true value to try and do the job using scientific name & rank if your ids aren't comparable to other dbs.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre