NAME
Smash::Utils::Tree - Object encapsulating a tree structure and associated functions.
SYNOPSIS
use Smash::Utils::Tree;
# make tree
my $tree = new Smash::Utils::Tree(NAME => "NCBI", TYPE => "phylogenetic");
# add root
my $root = new Smash::Utils::Tree::Node(ID => 1, \
NAME => "root", \
RANK => "no rank", \
PARENT => -10000);
$tree->add_node($root);
$tree->set_root($root);
# add a child to the root
my $bacteria = new Smash::Utils::Tree::Node(ID => 2, \
NAME => "Bacteria", \
RANK => "superkingdom");
$tree->add_node($bacteria);
$root->add_child($bacteria);
my $bac_chlor = new Smash::Utils::Tree::Node(ID => 3, \
NAME => "Bacteroidetes/Chlorobi", \
RANK => "superphylum");
$tree->add_node($bac_chlor);
$bacteria->add_child($bac_chlor);
my $bacteroidetes = new Smash::Utils::Tree::Node(ID => 4, \
NAME => "Bacteroidetes", \
RANK => "phylum");
$tree->add_node($bacteroidetes);
$bac_chlor->add_child($bacteroidetes);
# get information for a node
my $node = $tree->nodes->{3};
$node->id; # 3
$node->rank; # superphylum
$node->name; # Bacteroidetes/Chlorobi
$node->newick_name; # Bacteroidetes_Chlorobi
DESCRIPTION
Smash:Utils::MatrixIO provides functions to read and write matrices stored as hashes.
FUNCTIONS
Properties
name- returns the name of the tree.
type- returns the type of the tree (commonly used are "phylogenetic" and "functional").
root- returns the id of the root of the tree.
rootlink- returns the link to the root of the tree.
nodes- returns the hash containing all nodes, indexed by the id's.
get_id_for_ranked_name($rank, $name)- returns the id of the node for a given name at the given rank. E.g.,
$tree->get_id_for_ranked_name("genus", "Bacteroides"); # returns 816 in NCBI tree
Tree manipulation functions
add_node($node)- adds the node to this tree.
remove_node($node)- removes the node from this tree.
count_leaves- Returns the number of leaf nodes.
delete_data- Deletes data at every node.
propagate_data_to_root($node_id, $value)- Propagates $value at DATA all the way upto root from the given node.
prune_tree- Prunes the tree so that nodes without values for the DATA field will be removed. Needs DATA to be set in the nodes to remain, otherwise the whole tree will disappear and it cannot be undone. For example, if you have a list of node-ids that you want to keep, then set DATA to 1 in each of these nodes, propagate it all the way up to ROOT, then prune the tree.
prune_tree_recursive- Internal recursive routine called by
prune_tree. remove_straight_links- Removes internal nodes with just one child. For example,
- In this case, C is connected to A directly and becomes
propagate_data_average- Propagate values set in the DATA field bottom-up by setting the value at a node as the average of its immediate children.
propagate_data_average_recursive- Internal recursive routine called by
propagate_data_average. print_newick- Prints the tree in Newick format. This prints the whole tree. If you want a subtree to be printed, prune the tree beforehand using the DATA field. For example, if you have a list of node-ids that you want to keep, then set DATA to 1 in each of these nodes, propagate it all the way up to ROOT, then prune the tree.
print_newick_recursive- Internal recursive routine called by
print_newick. print_tree- Prints the tree in XML format.
print_tree_recursive- Internal recursive routine called by
print_tree. print_data- Prints the tree in XML format, only for nodes with DATA being set. Similar to
print_tree. print_data_recursive- Internal recursive routine called by
print_data. dump_tree- Dumps two files: names.dmp and nodes.dmp in NCBI taxonomy dump format corresponding to the tree.
|
____|____
| |
| |
A |
| |
| |
B |
| |
| |
C D
|
____|____
| |
| |
| |
| |
| |
| |
| |
| |
C D
Phylogenetic tree-specific functions
get_full_lineage()- returns list containing the ids of all the ancestral nodes in order (bottom-to-top).
get_full_lineage_string_for_id()- returns the taxonomic lineage as string in the following format:
get_common_ancestor()- returns the lowest common ancestor (LCA) for a given list of node ids (calls one of the two versions specified below).
get_common_ancestor_for_two()- returns the lowest common ancestor (LCA) for a given list of exactly two node ids.
get_common_ancestor_generic()- returns the lowest common ancestor (LCA) for a given list of node ids.
<lineage superkingdom="Bacteria" phylum="Bacteroidetes">
NAME
Smash::Utils::Tree::Node - Object encapsulating the node of a tree structure.
DESCRIPTION
FUNCTIONS
Properties of the object and methods.
Properties
id- returns taxonomy id.
name- returns the name of the organism at the node.
newick_name- returns the name that is newick compatible.
rank- returns the rank of the organism at the node.
parent- returns the id of the parent node.
parentlink- returns the parent node object.
nchildren- returns the number of children.
children- returns the hash containing all children nodes.
data- returns the data stored at the given node.
Tree manipulation functions
add_child($child)- add the given node to the children of this node.
remove_child($child)- removes the given from the children of this node.
copy_node()- returns a new
Smash::Utils::Tree::Nodeobject that is an exact copy of this node.
