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Manual Reference Pages  -  BIO::TAXONOMY::FACTORYI (3)

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NAME

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

CONTENTS

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.



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perl v5.20.3 BIO::TAXONOMY::FACTORYI (3) 2016-04-05

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