Bio::Taxonomy
FactoryI
Summary
Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
No synopsis!
Description
$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.
Methods
Methods description
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' |
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 |
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. |
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. |
Methods code
sub fetch
{ shift->throw_not_implemented; } | sub fuzzy_fetch
{ shift->throw_not_implemented; } | sub fetch_parent
{ shift->throw_not_implemented; } | sub fetch_children
{ shift->throw_not_implemented; } | General documentation
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The rest of the documentation details each of the object methods.
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