Bio::Taxonomy::FactoryI.3pm

Langue: en

Version: 2009-03-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy

DESCRIPTION

NB: This module has been deprecated.

$factory->fetch is a general method to fetch Taxonomy by either NCBI taxid or any types of names.

$factory->fetch_parent($taxonomy), returns a Taxonomy that is one-step higher rank of the taxonomy specified as argument.

$factory->fetch_children($taxonomy), reports an array of Taxonomy those are one-step lower rank of the taxonomy specified as the argument.

AUTHOR - Juguang Xiao

juguang@tll.org.sg

CONTRIBUTORS

Additional contributors' names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

fetch

   Title:    fetch
   Usage:    my $taxonomy = $factory->fetch(-taxon_id => 9605);
             my $taxonomy = $factory->fetch(-common_name => 'mammals');
   Fuctnion: Fetch taxonomy by taxon_id, common name or scientific name.
   Returns:  an instance of Bio::Taxonomy
   Args:     -taxon_id => NCBI taxonomy ID
             -common_name => comon name, such as 'human', 'mammals'
             -scientifc_name => specitic name, such as 'sapiens', 'Mammalia'
 
 

fuzzy_fetch

   Title:    fuzzy_fetch
   Usage:    my @taxonomy = $factory->fuzzy_fetch(-name => 'mouse');
   Function: Fuzzy fetch by name, or any text information found in DB
   Returns:  an array reference of Bio::Taxonomy objects
   Args:     -name => any name, such as common name, variant, scientific name
             -description, or -desc => any text information
 
 

fetch_parent

   Title:    fetch_parent
   Usage:    my $parent_taxonomy = $factory->fetch_parent($taxonomy);
   Function: Fetch the parent that is one-rank higher than the argument.
   Returns:  an instance of Bio::Taxonomy, or undef if the arg is the top one.
   Args:     a Bio::Taxonomy object.
 
 

fetch_children

   Title:    fetch_children
   Usage:    my @children_taxonomy = $factory->fetch_children($taxonomy);
   Function: Fetch all children those are one-rank lower than the argument.
   Returns:  an array reference of Bio::Taxonomy objects
   Args:     a Bio::Taxonomy object.