Package Bio :: Package Phylo :: Module BaseTree :: Class TreeMixin
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Class TreeMixin

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object --+
         |
        TreeMixin
Known Subclasses:

Methods for Tree- and Clade-based classes.

This lets Tree and Clade support the same traversal and searching operations without requiring Clade to inherit from Tree, so Clade isn't required to have all of Tree's attributes -- just root (a Clade instance) and is_terminal.

Instance Methods [hide private]
 
_filter_search(self, filter_func, order, follow_attrs)
Perform a BFS or DFS traversal through all elements in this tree.
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find_any(self, *args, **kwargs)
Return the first element found by find_elements(), or None.
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find_elements(self, target=None, terminal=None, order='preorder', **kwargs)
Find all tree elements matching the given attributes.
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find_clades(self, target=None, terminal=None, order='preorder', **kwargs)
Find each clade containing a matching element.
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get_path(self, target=None, **kwargs)
List the clades directly between this root and the given target.
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get_nonterminals(self, order='preorder')
Get a list of all of this tree's nonterminal (internal) nodes.
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get_terminals(self, order='preorder')
Get a list of all of this tree's terminal (leaf) nodes.
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trace(self, start, finish)
List of all clade object between two targets in this tree.
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common_ancestor(self, targets, *more_targets)
Most recent common ancestor (clade) of all the given targets.
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count_terminals(self)
Counts the number of terminal (leaf) nodes within this tree.
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depths(self, unit_branch_lengths=False)
Create a mapping of tree clades to depths (by branch length).
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distance(self, target1, target2=None)
Calculate the sum of the branch lengths between two targets.
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is_bifurcating(self)
Return True if tree downstream of node is strictly bifurcating.
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is_monophyletic(self, terminals, *more_terminals)
MRCA of terminals if they comprise a complete subclade, or False.
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is_parent_of(self, target=None, **kwargs)
True if target is a descendent of this tree.
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is_preterminal(self)
True if all direct descendents are terminal.
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total_branch_length(self)
Calculate the sum of all the branch lengths in this tree.
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collapse(self, target=None, **kwargs)
Deletes target from the tree, relinking its children to its parent.
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collapse_all(self, target=None, **kwargs)
Collapse all the descendents of this tree, leaving only terminals.
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ladderize(self, reverse=False)
Sort clades in-place according to the number of terminal nodes.
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prune(self, target=None, **kwargs)
Prunes a terminal clade from the tree.
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split(self, n=2, branch_length=1.0)
Generate n (default 2) new descendants.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __init__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

_filter_search(self, filter_func, order, follow_attrs)

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Perform a BFS or DFS traversal through all elements in this tree.
Returns:
generator of all elements for which filter_func is True.

find_any(self, *args, **kwargs)

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Return the first element found by find_elements(), or None.

This is also useful for checking whether any matching element exists in the tree, and can be used in a conditional expression.

find_elements(self, target=None, terminal=None, order='preorder', **kwargs)

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Find all tree elements matching the given attributes.

The arbitrary keyword arguments indicate the attribute name of the sub-element and the value to match: string, integer or boolean. Strings are evaluated as regular expression matches; integers are compared directly for equality, and booleans evaluate the attribute's truth value (True or False) before comparing. To handle nonzero floats, search with a boolean argument, then filter the result manually.

If no keyword arguments are given, then just the class type is used for matching.

The result is an iterable through all matching objects, by depth-first search. (Not necessarily the same order as the elements appear in the source file!)

Example

>>> from Bio.Phylo.IO import PhyloXMIO
>>> phx = PhyloXMLIO.read('phyloxml_examples.xml')
>>> matches = phx.phylogenies[5].find_elements(code='OCTVU')
>>> next(matches)
Taxonomy(code='OCTVU', scientific_name='Octopus vulgaris')
Parameters:
  • target (TreeElement instance, type, dict, or callable) - Specifies the characteristics to search for. (The default, TreeElement, matches any standard Bio.Phylo type.)
  • terminal (bool) - A boolean value to select for or against terminal nodes (a.k.a. leaf nodes). True searches for only terminal nodes, False excludes terminal nodes, and the default, None, searches both terminal and non-terminal nodes, as well as any tree elements lacking the is_terminal method.
  • order ({'preorder', 'postorder', 'level'}) - Tree traversal order: 'preorder' (default) is depth-first search, 'postorder' is DFS with child nodes preceding parents, and 'level' is breadth-first search.

find_clades(self, target=None, terminal=None, order='preorder', **kwargs)

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Find each clade containing a matching element.

That is, find each element as with find_elements(), but return the corresponding clade object. (This is usually what you want.)

Returns:
an iterable through all matching objects, searching depth-first (preorder) by default.

get_path(self, target=None, **kwargs)

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List the clades directly between this root and the given target.
Returns:
list of all clade objects along this path, ending with the given target, but excluding the root clade.

trace(self, start, finish)

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List of all clade object between two targets in this tree.

Excluding start, including finish.

common_ancestor(self, targets, *more_targets)

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Most recent common ancestor (clade) of all the given targets.

Edge cases: - If no target is given, returns self.root - If 1 target is given, returns the target - If any target is not found in this tree, raises a ValueError

depths(self, unit_branch_lengths=False)

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Create a mapping of tree clades to depths (by branch length).
Parameters:
  • unit_branch_lengths (bool) - If True, count only the number of branches (levels in the tree). By default the distance is the cumulative branch length leading to the clade.
Returns:
dict of {clade: depth}, where keys are all of the Clade instances in the tree, and values are the distance from the root to each clade (including terminals).

distance(self, target1, target2=None)

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Calculate the sum of the branch lengths between two targets.

If only one target is specified, the other is the root of this tree.

is_bifurcating(self)

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Return True if tree downstream of node is strictly bifurcating.

I.e., all nodes have either 2 or 0 children (internal or external, respectively). The root may have 3 descendents and still be considered part of a bifurcating tree, because it has no ancestor.

is_monophyletic(self, terminals, *more_terminals)

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MRCA of terminals if they comprise a complete subclade, or False.

I.e., there exists a clade such that its terminals are the same set as the given targets.

The given targets must be terminals of the tree.

To match both Bio.Nexus.Trees and the other multi-target methods in Bio.Phylo, arguments to this method can be specified either of two ways: (i) as a single list of targets, or (ii) separately specified targets, e.g. is_monophyletic(t1, t2, t3) -- but not both.

For convenience, this method returns the common ancestor (MCRA) of the targets if they are monophyletic (instead of the value True), and False otherwise.

Returns:
common ancestor if terminals are monophyletic, otherwise False.

is_parent_of(self, target=None, **kwargs)

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True if target is a descendent of this tree.

Not required to be a direct descendent.

To check only direct descendents of a clade, simply use list membership testing: if subclade in clade: ...

collapse(self, target=None, **kwargs)

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Deletes target from the tree, relinking its children to its parent.
Returns:
the parent clade.

collapse_all(self, target=None, **kwargs)

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Collapse all the descendents of this tree, leaving only terminals.

Total branch lengths are preserved, i.e. the distance to each terminal stays the same.

For example, this will safely collapse nodes with poor bootstrap support:

>>> tree.collapse_all(lambda c: c.confidence is not None and
...                   c.confidence < 70)

This implementation avoids strange side-effects by using level-order traversal and testing all clade properties (versus the target specification) up front. In particular, if a clade meets the target specification in the original tree, it will be collapsed. For example, if the condition is:

>>> tree.collapse_all(lambda c: c.branch_length < 0.1)

Collapsing a clade's parent node adds the parent's branch length to the child, so during the execution of collapse_all, a clade's branch_length may increase. In this implementation, clades are collapsed according to their properties in the original tree, not the properties when tree traversal reaches the clade. (It's easier to debug.) If you want the other behavior (incremental testing), modifying the source code of this function is straightforward.

ladderize(self, reverse=False)

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Sort clades in-place according to the number of terminal nodes.

Deepest clades are last by default. Use reverse=True to sort clades deepest-to-shallowest.

prune(self, target=None, **kwargs)

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Prunes a terminal clade from the tree.

If taxon is from a bifurcation, the connecting node will be collapsed and its branch length added to remaining terminal node. This might be no longer be a meaningful value.

Returns:
parent clade of the pruned target

split(self, n=2, branch_length=1.0)

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Generate n (default 2) new descendants.

In a species tree, this is a speciation event.

New clades have the given branch_length and the same name as this clade's root plus an integer suffix (counting from 0). For example, splitting a clade named "A" produces sub-clades named "A0" and "A1". If the clade has no name, the prefix "n" is used for child nodes, e.g. "n0" and "n1".