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|
#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Tree test data generation and verification.
"""
import sys
import dendropy
###############################################################################
## Test Tree
# Following tree:
#
# a
# / \
# / \
# / \
# / \
# / \
# / \
# / c
# b / \
# / \ / \
# / e / f
# / / \ / / \
# / / \ g / h
# / / \ / \ / / \
# i j k l m n o p
#
# Can be specified as:
#
# a -> b -> i;
# b -> e -> j;
# e -> k;
# a -> c;
# c -> g;
# c -> f;
# g -> l;
# g -> m;
# f -> n;
# f -> h -> o;
# h -> p;
class CuratedTestTree(object):
dot_str = "a -> b -> i; b -> e -> j; e -> k; a -> c; c -> g; c -> f; g -> l; g -> m; f -> n; f -> h -> o; h -> p;"
newick_unweighted_edges_str = "((i, (j, k)e)b, ((l, m)g, (n, (o, p)h)f)c)a;"
newick_weighted_edges_str = "((i:17, (j:3, k:3)e:14)b:33, ((l:6, m:6)g:30, (n:23, (o:11, p:11)h:12)f:13)c:14)a:15;"
preorder_sequence = ("a", "b", "i", "e", "j", "k", "c", "g", "l", "m", "f", "n", "h", "o", "p",)
postorder_sequence = ("i", "j", "k", "e", "b", "l", "m", "g", "n", "o", "p", "h", "f", "c", "a",)
leaf_sequence = ("i", "j", "k", "l", "m", "n", "o", "p",)
levelorder_sequence = ("a", "b", "c", "i", "e", "g", "f", "j", "k", "l", "m", "n", "h", "o", "p",)
internal_levelorder_sequence = ("a", "bc", "egf", "h",)
inorder_sequence = ("i", "b", "j", "e", "k", "a", "l", "g", "m", "c", "n", "f", "o", "h", "p",)
ageorder_sequence = ("i", "j", "k", "l", "m", "n", "o", "p", "e", "g", "h", "b", "f", "c", "a",)
leaf_labels = ( "i", "j", "k", "l", "m", "n", "o", "p",)
internal_labels = ( "a", "b", "c", "e", "f", "g", "h",)
all_labels = ( "a", "b", "c", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", )
node_children = {
"a" : ("b", "c",),
"b" : ("i", "e",),
"c" : ("g", "f",),
"e" : ("j", "k",),
"f" : ("n", "h",),
"g" : ("l", "m",),
"h" : ("o", "p",),
"i" : (),
"j" : (),
"k" : (),
"l" : (),
"m" : (),
"n" : (),
"o" : (),
"p" : (),
}
node_siblings = {
"a": (),
"b": ("c",),
"c": (),
"e": (),
"f": (),
"g": ("f",),
"h": (),
"i": ("e",),
"j": ("k",),
"k": (),
"l": ("m",),
"m": (),
"n": ("h",),
"o": ("p",),
"p": (),
}
node_edge_lengths = {
"a": 15.0,
"b": 33.0,
"c": 14.0,
"e": 14.0,
"f": 13.0,
"g": 30.0,
"h": 12.0,
"i": 17.0,
"j": 3.0,
"k": 3.0,
"l": 6.0,
"m": 6.0,
"n": 23.0,
"o": 11.0,
"p": 11.0,
}
node_ages = {
"a": 50.0,
"b": 17.0,
"c": 36.0,
"e": 3.0,
"f": 23.0,
"g": 6.0,
"h": 11.0,
"i": 0.0,
"j": 0.0,
"k": 0.0,
"l": 0.0,
"m": 0.0,
"n": 0.0,
"o": 0.0,
"p": 0.0,
}
node_ancestors = {
"a": (),
"b": ("a",),
"c": ("a",),
"e": ("b", "a",),
"f": ("c", "a",),
"g": ("c", "a",),
"h": ("f", "c", "a",),
"i": ("b", "a",),
"j": ("e", "b", "a",),
"k": ("e", "b", "a",),
"l": ("g", "c", "a",),
"m": ("g", "c", "a",),
"n": ("f", "c", "a",),
"o": ("h", "f", "c", "a",),
"p": ("h", "f", "c", "a",),
}
# def get_tree(self):
# tree = dendropy.Tree()
# def add_child_node(parent, label, edge_length):
# nd = tree.node_factory()
# nd.label = label
# nd.edge.length = edge_length
# parent.add_child(nd)
# return nd
# a = tree.seed_node
# a.label = "a"
# a.edge.length = 15.0
# b = add_child_node(a, label="b", edge_length=xxx["b"])
# c = add_child_node(a, label="c", edge_length=xxx["c"])
# e = add_child_node(b, label="i", edge_length=xxx["i"])
# i = add_child_node(b, label="c", edge_length=xxx["c"])
# j = add_child_node(e, label="j", edge_length=xxx["j"])
# k = add_child_node(e, label="k", edge_length=xxx["k"])
# f = add_child_node(c, label="f", edge_length=xxx["f"])
# g = add_child_node(c, label="g", edge_length=xxx["g"])
# l = add_child_node(g, label="l", edge_length=xxx["l"])
# m = add_child_node(g, label="m", edge_length=xxx["m"])
# h = add_child_node(f, label="h", edge_length=xxx["h"])
# n = add_child_node(f, label="n", edge_length=xxx["n"])
# o = add_child_node(h, label="o", edge_length=xxx["o"])
# p = add_child_node(h, label="p", edge_length=xxx["p"])
# return tree
def get_tree(self,
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=True,
taxon_namespace=None,
node_taxon_label_map=None,
):
if node_taxon_label_map is None:
node_taxon_label_map = {}
tree = dendropy.Tree(taxon_namespace=taxon_namespace)
a = tree.seed_node
a.label = "a"
a.edge.length = 15.0
b = a.new_child(label="b", edge_length=self.node_edge_lengths["b"])
assert b.label == "b"
assert b.edge.length == self.node_edge_lengths[b.label]
assert b.parent_node is a
assert b.edge.tail_node is a
assert b in a._child_nodes
c = a.new_child(label="c", edge_length=self.node_edge_lengths["c"])
assert c.label == "c"
assert c.edge.length == self.node_edge_lengths[c.label]
assert c.parent_node is a
assert c.edge.tail_node is a
assert c in a._child_nodes
i = b.new_child(label="i", edge_length=self.node_edge_lengths["i"])
assert i.label == "i"
assert i.edge.length == self.node_edge_lengths[i.label]
assert i.parent_node is b
assert i.edge.tail_node is b
assert i in b._child_nodes
e = b.new_child(label="e", edge_length=self.node_edge_lengths["e"])
assert e.label == "e"
assert e.edge.length == self.node_edge_lengths[e.label]
assert e.parent_node is b
assert e.edge.tail_node is b
assert e in b._child_nodes
j = e.new_child(label="j", edge_length=self.node_edge_lengths["j"])
assert j.label == "j"
assert j.edge.length == self.node_edge_lengths[j.label]
assert j.parent_node is e
assert j.edge.tail_node is e
assert j in e._child_nodes
k = e.new_child(label="k", edge_length=self.node_edge_lengths["k"])
assert k.label == "k"
assert k.edge.length == self.node_edge_lengths[k.label]
assert k.parent_node is e
assert k.edge.tail_node is e
assert k in e._child_nodes
g = c.new_child(label="g", edge_length=self.node_edge_lengths["g"])
assert g.label == "g"
assert g.edge.length == self.node_edge_lengths[g.label]
assert g.parent_node is c
assert g.edge.tail_node is c
assert g in c._child_nodes
f = c.new_child(label="f", edge_length=self.node_edge_lengths["f"])
assert f.label == "f"
assert f.edge.length == self.node_edge_lengths[f.label]
assert f.parent_node is c
assert f.edge.tail_node is c
assert f in c._child_nodes
l = g.new_child(label="l", edge_length=self.node_edge_lengths["l"])
assert l.label == "l"
assert l.edge.length == self.node_edge_lengths[l.label]
assert l.parent_node is g
assert l.edge.tail_node is g
assert l in g._child_nodes
m = g.new_child(label="m", edge_length=self.node_edge_lengths["m"])
assert m.label == "m"
assert m.edge.length == self.node_edge_lengths[m.label]
assert m.parent_node is g
assert m.edge.tail_node is g
assert m in g._child_nodes
n = f.new_child(label="n", edge_length=self.node_edge_lengths["n"])
assert n.label == "n"
assert n.edge.length == self.node_edge_lengths[n.label]
assert n.parent_node is f
assert n.edge.tail_node is f
assert n in f._child_nodes
h = f.new_child(label="h", edge_length=self.node_edge_lengths["h"])
assert h.label == "h"
assert h.edge.length == self.node_edge_lengths[h.label]
assert h.parent_node is f
assert h.edge.tail_node is f
assert h in f._child_nodes
o = h.new_child(label="o", edge_length=self.node_edge_lengths["o"])
assert o.label == "o"
assert o.edge.length == self.node_edge_lengths[o.label]
assert o.parent_node is h
assert o.edge.tail_node is h
assert o in h._child_nodes
p = h.new_child(label="p", edge_length=self.node_edge_lengths["p"])
assert p.label == "p"
assert p.edge.length == self.node_edge_lengths[p.label]
assert p.parent_node is h
assert p.edge.tail_node is h
assert p in h._child_nodes
tree._debug_check_tree()
leaf_nodes = set([i, j, k, l, m, n, o, p])
internal_nodes = set([b, c, e, f, g, h])
all_nodes = leaf_nodes | internal_nodes | set([a])
if not suppress_internal_node_taxa:
for nd in internal_nodes | set([a]):
label = node_taxon_label_map.get(nd.label, nd.label) # default to same label as node
t = tree.taxon_namespace.require_taxon(label=label)
nd.taxon = t
assert t in tree.taxon_namespace
if not suppress_leaf_node_taxa:
for nd in leaf_nodes:
label = node_taxon_label_map.get(nd.label, nd.label) # default to same label as node
t = tree.taxon_namespace.require_taxon(label=label)
nd.taxon = t
assert t in tree.taxon_namespace
return tree, all_nodes, leaf_nodes, internal_nodes
def verify_curated_tree(self,
tree,
suppress_internal_node_taxa=True,
suppress_leaf_node_taxa=False,
suppress_edge_lengths=False,
node_taxon_label_map=None):
if node_taxon_label_map is None:
node_taxon_label_map = {}
for nd, exp_nd in zip(tree, self.preorder_sequence):
if ( (nd.is_leaf() and suppress_leaf_node_taxa)
or ((not nd.is_leaf()) and suppress_internal_node_taxa) ):
label = nd.label
else:
self.assertIsNot(nd.taxon, None)
label = nd.taxon.label
self.assertEqual(label, node_taxon_label_map.get(exp_nd, exp_nd))
if suppress_edge_lengths:
self.assertIs(nd.edge.length, None)
else:
self.assertEqual(nd.edge.length, self.node_edge_lengths[exp_nd])
nd.canonical_label = exp_nd
for nd in tree:
children = [c.canonical_label for c in nd.child_node_iter()]
self.assertCountEqual(children, self.node_children[nd.canonical_label])
if nd.parent_node is None:
self.assertEqual(len(self.node_ancestors[nd.canonical_label]), 0)
else:
self.assertEqual(nd.parent_node.canonical_label,
self.node_ancestors[nd.canonical_label][0])
def get_newick_string(self,
suppress_edge_lengths=False,
node_taxon_label_map=None,
edge_label_compose_fn=None,
tree_preamble_tokens=None):
node_tag = {}
if node_taxon_label_map is None:
node_taxon_label_map = {}
if edge_label_compose_fn is None:
edge_label_compose_fn = lambda e: "{:6.5E}".format(e)
node_tag = {}
for nd in self.preorder_sequence:
label = node_taxon_label_map.get(nd, nd) # default to same label as node
if suppress_edge_lengths:
node_tag[nd] = label
else:
node_tag[nd] = "{}:{}".format(label, edge_label_compose_fn(self.node_edge_lengths[nd]))
if tree_preamble_tokens is None:
node_tag["preamble"] = ""
else:
node_tag["preamble"] = tree_preamble_tokens
s = "{preamble}(({i}, ({j}, {k}){e}){b}, (({l}, {m}){g}, ({n}, ({o}, {p}){h}){f}){c}){a};".format(
**node_tag
)
return s
|
