BP_TAXONOMY2TREE(1p) User Contributed Perl Documentation BP_TAXONOMY2TREE(1p)NAME
taxonomy2tree - Building a taxonomic tree based on the full lineages of a set of species names
DESCRIPTION
taxonomy2tree.PLS: -s Orangutan -s Gorilla -s Chimpanzee -s Human taxonomy2tree.PLS: -s Orangutan -s Gorilla -s Chimpanzee -s "Homo
Sapiens"
Can also provide -d to specific the directory to store index files in, -o to specific the location of your nodes file, and -a for the names
file. Or the option -e to use the web-based entrez taxonomy database if you don't have the flatfiles installed.
This script requires that the bioperl-run pkg be also installed.
Providing the nodes.dmp and names.dmp files from the NCBI Taxonomy dump (see Bio::DB::Taxonomy::flatfile for more info) is only necessary
on the first time running. This will create the local indexes and may take quite a long time. However once created, these indexes will
allow fast access for species to taxon id OR taxon id to species name lookups.
AUTHOR - Gabriel Valiente, reimplemented by Sendu Bala
Email valiente@lsi.upc.edu Email bix@sendu.me.uk
perl v5.14.2 2012-03-02 BP_TAXONOMY2TREE(1p)
Check Out this Related Man Page
Bio::Taxonomy(3pm) User Contributed Perl Documentation Bio::Taxonomy(3pm)NAME
Bio::Taxonomy - representing Taxonomy.
SYNOPSIS
# NB: This module is deprecated. Use Bio::Taxon in combination with
# Bio::Tree::Tree methods instead.
use Bio::Taxonomy;
# CREATION: You can either create an instance by assigning it,
# or fetch it through factory.
# Create the nodes first. See Bio::Taxonomy::Node for details.
my $node_species_sapiens = Bio::Taxonomy::Node->new(
-object_id => 9606, # or -ncbi_taxid. Requird tag
-names => {
'scientific' => ['sapiens'],
'common_name' => ['human']
},
-rank => 'species' # Required tag
);
my $node_genus_Homo = Bio::Taxonomy::Node->new(
-object_id => 9605,
-names => { 'scientific' => ['Homo'] },
-rank => 'genus'
);
my $node_class_Mammalia = Bio::Taxonomy::Node->new(
-object_id => 40674,
-names => {
'scientific' => ['Mammalia'],
'common' => ['mammals']
},
-rank => 'class'
);
my $taxonomy = Bio::Taxonomy->new;
$taxonomy->add_node($node_class_Mammalia);
$taxonomy->add_node($node_species_sapiens);
$taxonomy->add_node($node_genus_Homo);
# OR you can fetch it through a factory implementing
# Bio::Taxonomy::FactoryI
my $factory;
my $taxonomy = $factory->fetch_by_ncbi_taxid(40674);
# USAGE
# In this case, binomial returns a defined value.
my $binomial = $taxonomy->binomial;
# 'common_names' refers to the lowest-rank node's common names, in
# array.
my @common_names = $taxonomy->common_names;
# 'get_node', will return undef if the rank is no defined in
# taxonomy object. It will throw error if the rank string is not
# defined, say 'species lah'.
my $node = $taxonomy->get_node('class');
my @nodes = $taxonomy->get_all_nodes;
# Also, you can search for parent and children nodes, if taxonomy
# comes with factory.
my $parent_taxonomy = $taxonomy->get_parent
DESCRIPTION
Bio::Taxonomy object represents any rank-level in taxonomy system, rather than Bio::Species which is able to represent only species-level.
There are two ways to create Taxonomy object, e.g. 1) instantiate an object and assign all nodes on your own code; and 2) fetch an object
by factory.
Creation by instantiation
The abstraction of Taxonomy is actually a hash in data structure term. The keys of the hash are the rank names, such as 'genus' and
'species', and the values are the instances of Bio::Taxonomy::Node.
Creation by Factory fetching
NCBI Taxonomy system is well accepted as the standard. The Taxonomy Factories in bioperl access this system, through HTTP to NCBI Entrez,
dump file, and advanced biosql database.
Bio::Taxonomy::FactoryI defines all methods that all implementations must obey.
$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.
Usage of Taxonomy object
##
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
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
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:
https://redmine.open-bio.org/projects/bioperl/
CONTACT
Juguang Xiao, juguang@tll.org.sg
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Taxonomy->new();
Function: Builds a new Bio::Taxonomy object
Returns : Bio::Taxonomy
Args : -method -> method used to decide classification
(none|trust|lookup)
-ranks -> what ranks are there
method
Title : method
Usage : $obj = taxonomy->method($method);
Function: set or return the method used to decide classification
Returns : $obj
Args : $obj
classify
Title : classify
Usage : @obj[][0-1] = taxonomy->classify($species);
Function: return a ranked classification
Returns : @obj of taxa and ranks as word pairs separated by "@"
Args : Bio::Species object
level_of_rank
Title : level_of_rank
Usage : $obj = taxonomy->level_of_rank($obj);
Function: returns the level of a rank name
Returns : $obj
Args : $obj
rank_of_number
Title : rank_of_number
Usage : $obj = taxonomy->rank_of_number($obj);
Function: returns the rank name of a rank level
Returns : $obj
Args : $obj
ranks
Title : ranks
Usage : @obj = taxonomy->ranks(@obj);
Function: set or return all ranks
Returns : @obj
Args : @obj
add_node
Title: add_node
Usage: $obj->add_node($node[, $node2, ...]);
Function: add one or more Bio::Taxonomy::Node objects
Returns: None
Args: any number of Bio::Taxonomy::Node(s)
binomial
Title : binomial
Usage : my $val = $obj->binomial;
Function: returns the binomial name if this taxonomy reachs species level
Returns : the binomial name
OR undef if taxonmy does not reach species level
Args : [No arguments]
get_node
Title : get_node
Usage : $node = $taxonomy->get_node('species');
Function: get a Bio::Taxonomy::Node object according to rank name
Returns : a Bio::Taxonomy::Node object or undef if null
Args : a vaild rank name
classification
Title : classification
Usage : @names = $taxonomy->classification;
Function: get the classification names of one taxonomy
Returns : array of names
Args : [No arguments]
perl v5.14.2 2012-03-02 Bio::Taxonomy(3pm)