Christopher Fields > BioPerl-1.6.901 > Bio::Taxonomy::FactoryI

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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924

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.
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