# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com) # # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". # Please see the LICENSE file that should have been included as part of this # package. """Base classes for Bio.Phylo objects. All object representations for phylogenetic trees should derive from these base classes in order to use the common methods defined on them. """ import collections import copy import itertools import random import re # General tree-traversal algorithms def _level_traverse(root, get_children): """Traverse a tree in breadth-first (level) order (PRIVATE).""" Q = collections.deque([root]) while Q: v = Q.popleft() yield v Q.extend(get_children(v)) def _preorder_traverse(root, get_children): """Traverse a tree in depth-first pre-order (parent before children) (PRIVATE).""" def dfs(elem): yield elem for v in get_children(elem): yield from dfs(v) yield from dfs(root) def _postorder_traverse(root, get_children): """Traverse a tree in depth-first post-order (children before parent) (PRIVATE).""" def dfs(elem): for v in get_children(elem): yield from dfs(v) yield elem yield from dfs(root) def _sorted_attrs(elem): """Get a flat list of elem's attributes, sorted for consistency (PRIVATE).""" singles = [] lists = [] # Sort attributes for consistent results for attrname, child in sorted(elem.__dict__.items(), key=lambda kv: kv[0]): if child is None: continue if isinstance(child, list): lists.extend(child) else: singles.append(child) return (x for x in singles + lists if isinstance(x, TreeElement)) # Factory functions to generalize searching for clades/nodes def _identity_matcher(target): """Match a node to the target object by identity (PRIVATE).""" def match(node): return node is target return match def _class_matcher(target_cls): """Match a node if it's an instance of the given class (PRIVATE).""" def match(node): return isinstance(node, target_cls) return match def _string_matcher(target): def match(node): if isinstance(node, (Clade, Tree)): # Avoid triggering specialized or recursive magic methods return node.name == target return str(node) == target return match def _attribute_matcher(kwargs): """Match a node by specified attribute values (PRIVATE). ``terminal`` is a special case: True restricts the search to external (leaf) nodes, False restricts to internal nodes, and None allows all tree elements to be searched, including phyloXML annotations. Otherwise, for a tree element to match the specification (i.e. for the function produced by ``_attribute_matcher`` to return True when given a tree element), it must have each of the attributes specified by the keys and match each of the corresponding values -- think 'and', not 'or', for multiple keys. """ def match(node): if "terminal" in kwargs: # Special case: restrict to internal/external/any nodes kwa_copy = kwargs.copy() pattern = kwa_copy.pop("terminal") if pattern is not None and ( not hasattr(node, "is_terminal") or node.is_terminal() != pattern ): return False else: kwa_copy = kwargs for key, pattern in kwa_copy.items(): # Nodes must match all other specified attributes if not hasattr(node, key): return False target = getattr(node, key) if isinstance(pattern, str): return isinstance(target, str) and re.match(pattern + "$", target) if isinstance(pattern, bool): return pattern == bool(target) if isinstance(pattern, int): return pattern == target if pattern is None: return target is None raise TypeError(f"invalid query type: {type(pattern)}") return True return match def _function_matcher(matcher_func): """Safer attribute lookup -- returns False instead of raising an error (PRIVATE).""" def match(node): try: return matcher_func(node) except (LookupError, AttributeError, ValueError, TypeError): return False return match def _object_matcher(obj): """Retrieve a matcher function by passing an arbitrary object (PRIVATE). Passing a ``TreeElement`` such as a ``Clade`` or ``Tree`` instance returns an identity matcher, passing a type such as the ``PhyloXML.Taxonomy`` class returns a class matcher, and passing a dictionary returns an attribute matcher. The resulting 'match' function returns True when given an object matching the specification (identity, type or attribute values), otherwise False. This is useful for writing functions that search the tree, and probably shouldn't be used directly by the end user. """ if isinstance(obj, TreeElement): return _identity_matcher(obj) if isinstance(obj, type): return _class_matcher(obj) if isinstance(obj, str): return _string_matcher(obj) if isinstance(obj, dict): return _attribute_matcher(obj) if callable(obj): return _function_matcher(obj) raise ValueError(f"{obj} (type {type(obj)}) is not a valid type for comparison.") def _combine_matchers(target, kwargs, require_spec): """Merge target specifications with keyword arguments (PRIVATE). Dispatch the components to the various matcher functions, then merge into a single boolean function. """ if not target: if not kwargs: if require_spec: raise ValueError( "you must specify a target object or keyword arguments." ) return lambda x: True return _attribute_matcher(kwargs) match_obj = _object_matcher(target) if not kwargs: return match_obj match_kwargs = _attribute_matcher(kwargs) return lambda x: match_obj(x) and match_kwargs(x) def _combine_args(first, *rest): """Convert ``[targets]`` or ``*targets`` arguments to a single iterable (PRIVATE). This helps other functions work like the built-in functions ``max`` and ``min``. """ # Background: is_monophyletic takes a single list or iterable (like the # same method in Bio.Nexus.Trees); root_with_outgroup and common_ancestor # take separate arguments. This mismatch was in the initial release and I # didn't notice the inconsistency until after Biopython 1.55. I can think # of cases where either style is more convenient, so let's support both # (for backward compatibility and consistency between methods). if hasattr(first, "__iter__") and not ( isinstance(first, (TreeElement, dict, str, type)) ): # terminals is an iterable of targets if rest: raise ValueError( "Arguments must be either a single list of " "targets, or separately specified targets " "(e.g. foo(t1, t2, t3)), but not both." ) return first # terminals is a single target -- wrap in a container return itertools.chain([first], rest) # Class definitions class TreeElement: """Base class for all Bio.Phylo classes.""" def __repr__(self) -> str: """Show this object's constructor with its primitive arguments.""" def pair_as_kwarg_string(key, val): if isinstance(val, str): val = val[:57] + "..." if len(val) > 60 else val return f"{key}='{val}'" return f"{key}={val}" return "%s(%s)" % ( self.__class__.__name__, ", ".join( pair_as_kwarg_string(key, val) for key, val in sorted(self.__dict__.items()) if val is not None and type(val) in (str, int, float, bool, str) ), ) def __str__(self) -> str: return self.__repr__() class TreeMixin: """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``. """ # Traversal methods def _filter_search(self, filter_func, order, follow_attrs): """Perform a BFS or DFS traversal through all elements in this tree (PRIVATE). :returns: generator of all elements for which ``filter_func`` is True. """ order_opts = { "preorder": _preorder_traverse, "postorder": _postorder_traverse, "level": _level_traverse, } try: order_func = order_opts[order] except KeyError: raise ValueError( f"Invalid order '{order}'; must be one of: {tuple(order_opts)}" ) from None if follow_attrs: get_children = _sorted_attrs root = self else: get_children = lambda elem: elem.clades # noqa: E731 root = self.root return filter(filter_func, order_func(root, get_children)) def find_any(self, *args, **kwargs): """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. """ hits = self.find_elements(*args, **kwargs) try: return next(hits) except StopIteration: return None def find_elements(self, target=None, terminal=None, order="preorder", **kwargs): """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!) :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. Examples -------- >>> from Bio import Phylo >>> phx = Phylo.PhyloXMLIO.read('PhyloXML/phyloxml_examples.xml') >>> matches = phx.phylogenies[5].find_elements(code='OCTVU') >>> next(matches) Taxonomy(code='OCTVU', scientific_name='Octopus vulgaris') """ if terminal is not None: kwargs["terminal"] = terminal is_matching_elem = _combine_matchers(target, kwargs, False) return self._filter_search(is_matching_elem, order, True) def find_clades(self, target=None, terminal=None, order="preorder", **kwargs): """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. """ def match_attrs(elem): orig_clades = elem.__dict__.pop("clades") found = elem.find_any(target, **kwargs) elem.clades = orig_clades return found is not None if terminal is None: is_matching_elem = match_attrs else: def is_matching_elem(elem): return (elem.is_terminal() == terminal) and match_attrs(elem) return self._filter_search(is_matching_elem, order, False) def get_path(self, target=None, **kwargs): """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. """ # Only one path will work -- ignore weights and visits path = [] match = _combine_matchers(target, kwargs, True) def check_in_path(v): if match(v): path.append(v) return True elif v.is_terminal(): return False for child in v: if check_in_path(child): path.append(v) return True return False if not check_in_path(self.root): return None return path[-2::-1] def get_nonterminals(self, order="preorder"): """Get a list of all of this tree's nonterminal (internal) nodes.""" return list(self.find_clades(terminal=False, order=order)) def get_terminals(self, order="preorder"): """Get a list of all of this tree's terminal (leaf) nodes.""" return list(self.find_clades(terminal=True, order=order)) def trace(self, start, finish): """List of all clade object between two targets in this tree. Excluding ``start``, including ``finish``. """ mrca = self.common_ancestor(start, finish) fromstart = mrca.get_path(start)[-2::-1] to = mrca.get_path(finish) return fromstart + [mrca] + to # Information methods def common_ancestor(self, targets, *more_targets): """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 """ paths = [self.get_path(t) for t in _combine_args(targets, *more_targets)] # Validation -- otherwise izip throws a spooky error below for p, t in zip(paths, targets): if p is None: raise ValueError(f"target {t!r} is not in this tree") mrca = self.root for level in zip(*paths): ref = level[0] for other in level[1:]: if ref is not other: break else: mrca = ref if ref is not mrca: break return mrca def count_terminals(self): """Count the number of terminal (leaf) nodes within this tree.""" return sum(1 for clade in self.find_clades(terminal=True)) def depths(self, unit_branch_lengths=False): # noqa: D402 """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). """ # noqa: D402 if unit_branch_lengths: depth_of = lambda c: 1 # noqa: E731 else: depth_of = lambda c: c.branch_length or 0 # noqa: E731 depths = {} def update_depths(node, curr_depth): depths[node] = curr_depth for child in node.clades: new_depth = curr_depth + depth_of(child) update_depths(child, new_depth) update_depths(self.root, self.root.branch_length or 0) return depths def distance(self, target1, target2=None): """Calculate the sum of the branch lengths between two targets. If only one target is specified, the other is the root of this tree. """ if target2 is None: return sum( n.branch_length for n in self.get_path(target1) if n.branch_length is not None ) mrca = self.common_ancestor(target1, target2) return mrca.distance(target1) + mrca.distance(target2) def is_bifurcating(self): """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. """ # Root can be trifurcating if isinstance(self, Tree) and len(self.root) == 3: return ( self.root.clades[0].is_bifurcating() and self.root.clades[1].is_bifurcating() and self.root.clades[2].is_bifurcating() ) if len(self.root) == 2: return ( self.root.clades[0].is_bifurcating() and self.root.clades[1].is_bifurcating() ) if len(self.root) == 0: return True return False def is_monophyletic(self, terminals, *more_terminals): """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. """ target_set = set(_combine_args(terminals, *more_terminals)) current = self.root while True: if set(current.get_terminals()) == target_set: return current # Try a narrower subclade for subclade in current.clades: if set(subclade.get_terminals()).issuperset(target_set): current = subclade break else: return False def is_parent_of(self, target=None, **kwargs): """Check 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: ...`` """ return self.get_path(target, **kwargs) is not None def is_preterminal(self): """Check if all direct descendents are terminal.""" if self.root.is_terminal(): return False for clade in self.root.clades: if not clade.is_terminal(): return False return True def total_branch_length(self): """Calculate the sum of all the branch lengths in this tree.""" return sum(node.branch_length for node in self.find_clades(branch_length=True)) # Tree manipulation methods def collapse(self, target=None, **kwargs): """Delete target from the tree, relinking its children to its parent. :returns: the parent clade. """ path = self.get_path(target, **kwargs) if not path: raise ValueError("couldn't collapse %s in this tree" % (target or kwargs)) if len(path) == 1: parent = self.root else: parent = path[-2] popped = parent.clades.pop(parent.clades.index(path[-1])) extra_length = popped.branch_length or 0 for child in popped: child.branch_length += extra_length parent.clades.extend(popped.clades) return parent def collapse_all(self, target=None, **kwargs): """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: >>> from Bio import Phylo >>> tree = Phylo.read('PhyloXML/apaf.xml', 'phyloxml') >>> print("Total branch length %0.2f" % tree.total_branch_length()) Total branch length 20.44 >>> tree.collapse_all(lambda c: c.confidence is not None and c.confidence < 70) >>> print("Total branch length %0.2f" % tree.total_branch_length()) Total branch length 21.37 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: >>> from Bio import Phylo >>> tree = Phylo.read('PhyloXML/apaf.xml', 'phyloxml') >>> print("Total branch length %0.2f" % tree.total_branch_length()) Total branch length 20.44 >>> tree.collapse_all(lambda c: c.branch_length < 0.1) >>> print("Total branch length %0.2f" % tree.total_branch_length()) Total branch length 21.13 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. """ # Read the iterable into a list to protect against in-place changes matches = list(self.find_clades(target, False, "level", **kwargs)) if not matches: # No matching nodes to collapse return # Skip the root node -- it can't be collapsed if matches[0] == self.root: matches.pop(0) for clade in matches: self.collapse(clade) def ladderize(self, reverse=False): """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. """ self.root.clades.sort(key=lambda c: c.count_terminals(), reverse=reverse) for subclade in self.root.clades: subclade.ladderize(reverse=reverse) def prune(self, target=None, **kwargs): """Prunes a terminal clade from the tree. If the taxon is from a bifurcation, the connecting node will be collapsed and its branch length added to remaining terminal node. This might no longer be a meaningful value. :returns: parent clade of the pruned target """ if "terminal" in kwargs and kwargs["terminal"]: raise ValueError("target must be terminal") path = self.get_path(target, terminal=True, **kwargs) if not path: raise ValueError("can't find a matching target below this root") if len(path) == 1: parent = self.root else: parent = path[-2] parent.clades.remove(path[-1]) if len(parent) == 1: # We deleted a branch from a bifurcation child = parent.clades[0] if child.branch_length is not None: child.branch_length += parent.branch_length or 0.0 if len(path) == 1: # If we're at the root, move the root upwards parent = self.root = child else: # If we're not at the root, collapse this parent if len(path) < 3: grandparent = self.root else: grandparent = path[-3] # Replace parent with child at the same place in grandparent index = grandparent.clades.index(parent) grandparent.clades.pop(index) grandparent.clades.insert(index, child) parent = grandparent return parent def split(self, n=2, branch_length=1.0): """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". """ clade_cls = type(self.root) base_name = self.root.name or "n" for i in range(n): clade = clade_cls(name=base_name + str(i), branch_length=branch_length) self.root.clades.append(clade) class Tree(TreeElement, TreeMixin): """A phylogenetic tree, containing global info for the phylogeny. The structure and node-specific data is accessible through the 'root' clade attached to the Tree instance. :Parameters: root : Clade The starting node of the tree. If the tree is rooted, this will usually be the root node. rooted : bool Whether or not the tree is rooted. By default, a tree is assumed to be rooted. id : str The identifier of the tree, if there is one. name : str The name of the tree, in essence a label. """ def __init__(self, root=None, rooted=True, id=None, name=None): """Initialize parameter for phylogenetic tree.""" self.root = root or Clade() self.rooted = rooted self.id = id self.name = name @classmethod def from_clade(cls, clade, **kwargs): """Create a new Tree object given a clade. Keyword arguments are the usual ``Tree`` constructor parameters. """ root = copy.deepcopy(clade) return cls(root, **kwargs) @classmethod def randomized(cls, taxa, branch_length=1.0, branch_stdev=None): """Create a randomized bifurcating tree given a list of taxa. :param taxa: Either an integer specifying the number of taxa to create (automatically named taxon#), or an iterable of taxon names, as strings. :returns: a tree of the same type as this class. """ if isinstance(taxa, int): taxa = [f"taxon{i + 1}" for i in range(taxa)] elif hasattr(taxa, "__iter__"): taxa = list(taxa) else: raise TypeError( "taxa argument must be integer (# taxa) or iterable of taxon names." ) rtree = cls() terminals = [rtree.root] while len(terminals) < len(taxa): newsplit = random.choice(terminals) newsplit.split(branch_length=branch_length) newterms = newsplit.clades if branch_stdev: # Add some noise to the branch lengths for nt in newterms: nt.branch_length = max(0, random.gauss(branch_length, branch_stdev)) terminals.remove(newsplit) terminals.extend(newterms) # Distribute taxon labels randomly random.shuffle(taxa) for node, name in zip(terminals, taxa): node.name = name return rtree @property def clade(self): """Return first clade in this tree (not itself).""" return self.root def as_phyloxml(self, **kwargs): """Convert this tree to a PhyloXML-compatible Phylogeny. This lets you use the additional annotation types PhyloXML defines, and save this information when you write this tree as 'phyloxml'. """ from Bio.Phylo.PhyloXML import Phylogeny return Phylogeny.from_tree(self, **kwargs) def root_with_outgroup( self, outgroup_targets, *more_targets, outgroup_branch_length=None ): """Reroot this tree with the outgroup clade containing outgroup_targets. Operates in-place. Edge cases: - If ``outgroup == self.root``, no change - If outgroup is terminal, create new bifurcating root node with a 0-length branch to the outgroup - If outgroup is internal, use the given outgroup node as the new trifurcating root, keeping branches the same - If the original root was bifurcating, drop it from the tree, preserving total branch lengths :param outgroup_branch_length: length of the branch leading to the outgroup after rerooting. If not specified (None), then: - If the outgroup is an internal node (not a single terminal taxon), then use that node as the new root. - Otherwise, create a new root node as the parent of the outgroup. """ # This raises a ValueError if any target is not in this tree # Otherwise, common_ancestor guarantees outgroup is in this tree outgroup = self.common_ancestor(outgroup_targets, *more_targets) outgroup_path = self.get_path(outgroup) if len(outgroup_path) == 0: # Outgroup is the current root -- no change return prev_blen = outgroup.branch_length or 0.0 if outgroup.is_terminal() or outgroup_branch_length is not None: # Create a new root with a 0-length branch to the outgroup outgroup.branch_length = outgroup_branch_length or 0.0 new_root = self.root.__class__( branch_length=self.root.branch_length, clades=[outgroup] ) # The first branch reversal (see the upcoming loop) is modified if len(outgroup_path) == 1: # No nodes between the original root and outgroup to rearrange. # Most of the code below will be skipped, but we still need # 'new_parent' pointing at the new root. new_parent = new_root else: parent = outgroup_path.pop(-2) # First iteration of reversing the path to the outgroup parent.clades.pop(parent.clades.index(outgroup)) (prev_blen, parent.branch_length) = ( parent.branch_length, prev_blen - outgroup.branch_length, ) new_root.clades.insert(0, parent) new_parent = parent else: # Use the given outgroup node as the new (trifurcating) root new_root = outgroup new_root.branch_length = self.root.branch_length new_parent = new_root # Tracing the outgroup lineage backwards, reattach the subclades under a # new root clade. Reverse the branches directly above the outgroup in # the tree, but keep the descendants of those clades as they are. for parent in outgroup_path[-2::-1]: parent.clades.pop(parent.clades.index(new_parent)) prev_blen, parent.branch_length = parent.branch_length, prev_blen new_parent.clades.insert(0, parent) new_parent = parent # Finally, handle the original root according to number of descendents old_root = self.root if outgroup in old_root.clades: assert len(outgroup_path) == 1 old_root.clades.pop(old_root.clades.index(outgroup)) else: old_root.clades.pop(old_root.clades.index(new_parent)) if len(old_root) == 1: # Delete the old bifurcating root & add branch lengths ingroup = old_root.clades[0] if ingroup.branch_length: ingroup.branch_length += prev_blen else: ingroup.branch_length = prev_blen new_parent.clades.insert(0, ingroup) # ENH: If annotations are attached to old_root, do... something. else: # Keep the old trifurcating/polytomous root as an internal node old_root.branch_length = prev_blen new_parent.clades.insert(0, old_root) self.root = new_root self.rooted = True def root_at_midpoint(self): """Root the tree at the midpoint of the two most distant taxa. This operates in-place, leaving a bifurcating root. The topology of the tree is otherwise retained, though no guarantees are made about the stability of clade/node/taxon ordering. """ # Identify the largest pairwise distance max_distance = 0.0 tips = self.get_terminals() for tip in tips: self.root_with_outgroup(tip) new_max = max(self.depths().items(), key=lambda nd: nd[1]) if new_max[1] > max_distance: tip1 = tip tip2 = new_max[0] max_distance = new_max[1] self.root_with_outgroup(tip1) # Depth to go from the ingroup tip toward the outgroup tip root_remainder = 0.5 * (max_distance - (self.root.branch_length or 0)) assert root_remainder >= 0 # Identify the midpoint and reroot there. # Trace the path to the outgroup tip until all of the root depth has # been traveled/accounted for. for node in self.get_path(tip2): root_remainder -= node.branch_length if root_remainder < 0: outgroup_node = node outgroup_branch_length = -root_remainder break else: raise ValueError("Somehow, failed to find the midpoint!") self.root_with_outgroup( outgroup_node, outgroup_branch_length=outgroup_branch_length ) # Method assumed by TreeMixin def is_terminal(self): """Check if the root of this tree is terminal.""" return not self.root.clades # Convention from SeqRecord and Alignment classes def __format__(self, format_spec): """Serialize the tree as a string in the specified file format. This method supports Python's ``format`` built-in function. :param format_spec: a lower-case string supported by ``Bio.Phylo.write`` as an output file format. """ if format_spec: from io import StringIO from Bio.Phylo import _io handle = StringIO() _io.write([self], handle, format_spec) return handle.getvalue() else: # Follow python convention and default to using __str__ return str(self) def format(self, fmt=None): """Serialize the tree as a string in the specified file format. :param fmt: a lower-case string supported by ``Bio.Phylo.write`` as an output file format. """ return self.__format__(fmt) # Pretty-printer for the entire tree hierarchy def __str__(self) -> str: """Return a string representation of the entire tree. Serialize each sub-clade recursively using ``repr`` to create a summary of the object structure. """ TAB = " " textlines = [] def print_tree(obj, indent): """Recursively serialize sub-elements. This closes over textlines and modifies it in-place. """ if isinstance(obj, (Tree, Clade)): # Avoid infinite recursion or special formatting from str() objstr = repr(obj) else: objstr = str(obj) textlines.append(TAB * indent + objstr) indent += 1 for attr in obj.__dict__: child = getattr(obj, attr) if isinstance(child, TreeElement): print_tree(child, indent) elif isinstance(child, list): for elem in child: if isinstance(elem, TreeElement): print_tree(elem, indent) print_tree(self, 0) return "\n".join(textlines) class Clade(TreeElement, TreeMixin): """A recursively defined sub-tree. :Parameters: branch_length : str The length of the branch leading to the root node of this clade. name : str The clade's name (a label). clades : list Sub-trees rooted directly under this tree's root. confidence : number Support. color : BranchColor The display color of the branch and descendents. width : number The display width of the branch and descendents. """ def __init__( self, branch_length=None, name=None, clades=None, confidence=None, color=None, width=None, ): """Define parameters for the Clade tree.""" self.branch_length = branch_length self.name = name self.clades = clades or [] self.confidence = confidence self.color = color self.width = width @property def root(self): """Allow TreeMixin methods to traverse clades properly.""" return self def is_terminal(self): """Check if this is a terminal (leaf) node.""" return not self.clades # Sequence-type behavior methods def __getitem__(self, index): """Get clades by index (integer or slice).""" if isinstance(index, (int, slice)): return self.clades[index] ref = self for idx in index: ref = ref[idx] return ref def __iter__(self): """Iterate through this tree's direct descendent clades (sub-trees).""" return iter(self.clades) def __len__(self): """Return the number of clades directly under the root.""" return len(self.clades) def __bool__(self): """Boolean value of an instance of this class (True). NB: If this method is not defined, but ``__len__`` is, then the object is considered true if the result of ``__len__()`` is nonzero. We want Clade instances to always be considered True. """ return True def __str__(self) -> str: """Return name of the class instance.""" if self.name: return self.name[:37] + "..." if len(self.name) > 40 else self.name return self.__class__.__name__ # Syntax sugar for setting the branch color def _get_color(self): return self._color def _set_color(self, arg): if arg is None or isinstance(arg, BranchColor): self._color = arg elif isinstance(arg, str): if arg in BranchColor.color_names: # Known color name self._color = BranchColor.from_name(arg) elif arg.startswith("#") and len(arg) == 7: # HTML-style hex string self._color = BranchColor.from_hex(arg) else: raise ValueError(f"invalid color string {arg}") elif hasattr(arg, "__iter__") and len(arg) == 3: # RGB triplet self._color = BranchColor(*arg) else: raise ValueError(f"invalid color value {arg}") color = property(_get_color, _set_color, doc="Branch color.") class BranchColor: """Indicates the color of a clade when rendered graphically. The color should be interpreted by client code (e.g. visualization programs) as applying to the whole clade, unless overwritten by the color(s) of sub-clades. Color values must be integers from 0 to 255. """ color_names = { "red": (255, 0, 0), "r": (255, 0, 0), "yellow": (255, 255, 0), "y": (255, 255, 0), "green": (0, 128, 0), "g": (0, 128, 0), "cyan": (0, 255, 255), "c": (0, 255, 255), "blue": (0, 0, 255), "b": (0, 0, 255), "magenta": (255, 0, 255), "m": (255, 0, 255), "black": (0, 0, 0), "k": (0, 0, 0), "white": (255, 255, 255), "w": (255, 255, 255), # Names standardized in HTML/CSS spec # http://w3schools.com/html/html_colornames.asp "maroon": (128, 0, 0), "olive": (128, 128, 0), "lime": (0, 255, 0), "aqua": (0, 255, 255), "teal": (0, 128, 128), "navy": (0, 0, 128), "fuchsia": (255, 0, 255), "purple": (128, 0, 128), "silver": (192, 192, 192), "gray": (128, 128, 128), # More definitions from matplotlib/gcolor2 "grey": (128, 128, 128), "pink": (255, 192, 203), "salmon": (250, 128, 114), "orange": (255, 165, 0), "gold": (255, 215, 0), "tan": (210, 180, 140), "brown": (165, 42, 42), } def __init__(self, red, green, blue): """Initialize BranchColor for a tree.""" for color in (red, green, blue): assert ( isinstance(color, int) and 0 <= color <= 255 ), "Color values must be integers between 0 and 255." self.red = red self.green = green self.blue = blue @classmethod def from_hex(cls, hexstr): """Construct a BranchColor object from a hexadecimal string. The string format is the same style used in HTML and CSS, such as '#FF8000' for an RGB value of (255, 128, 0). """ assert ( isinstance(hexstr, str) and hexstr.startswith("#") and len(hexstr) == 7 ), "need a 24-bit hexadecimal string, e.g. #000000" RGB = hexstr[1:3], hexstr[3:5], hexstr[5:] return cls(*(int("0x" + cc, base=16) for cc in RGB)) @classmethod def from_name(cls, colorname): """Construct a BranchColor object by the color's name.""" return cls(*cls.color_names[colorname]) def to_hex(self): """Return a 24-bit hexadecimal RGB representation of this color. The returned string is suitable for use in HTML/CSS, as a color parameter in matplotlib, and perhaps other situations. Examples -------- >>> bc = BranchColor(12, 200, 100) >>> bc.to_hex() '#0cc864' """ return f"#{self.red:02x}{self.green:02x}{self.blue:02x}" def to_rgb(self): """Return a tuple of RGB values (0 to 255) representing this color. Examples -------- >>> bc = BranchColor(255, 165, 0) >>> bc.to_rgb() (255, 165, 0) """ return (self.red, self.green, self.blue) def __repr__(self) -> str: """Preserve the standard RGB order when representing this object.""" return "%s(red=%d, green=%d, blue=%d)" % ( self.__class__.__name__, self.red, self.green, self.blue, ) def __str__(self) -> str: """Show the color's RGB values.""" return "(%d, %d, %d)" % (self.red, self.green, self.blue)