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"""Unit tests for tree parsers.
"""
from unittest import TestCase
from cogent3.core.tree import PhyloNode
from cogent3.parse.tree import DndParser, DndTokenizer, RecordError
sample = """
(
(
xyz:0.28124,
(
def:0.24498,
mno:0.03627)
:0.17710)
:0.04870,
abc:0.05925,
(
ghi:0.06914,
jkl:0.13776)
:0.09853);
"""
node_data_sample = """
(
(
xyz:0.28124,
(
def:0.24498,
mno:0.03627)
'A':0.17710)
B:0.04870,
abc:0.05925,
(
ghi:0.06914,
jkl:0.13776)
C:0.09853);
"""
minimal = "();"
no_names = "((,),(,));"
missing_tip_name = "((a,b),(c,));"
empty = "();"
single = "(abc:3);"
double = "(abc:3, def:4);"
onenest = "(abc:3, (def:4, ghi:5):6 );"
nodedata = "(abc:3, (def:4, ghi:5)jkl:6 );"
class DndTokenizerTests(TestCase):
"""Tests of the DndTokenizer factory function."""
def test_gdata(self):
"""DndTokenizer should work as expected on real data"""
exp = [
"(",
"(",
"xyz",
":",
"0.28124",
",",
"(",
"def",
":",
"0.24498",
",",
"mno",
":",
"0.03627",
")",
":",
"0.17710",
")",
":",
"0.04870",
",",
"abc",
":",
"0.05925",
",",
"(",
"ghi",
":",
"0.06914",
",",
"jkl",
":",
"0.13776",
")",
":",
"0.09853",
")",
";",
]
# split it up for debugging on an item-by-item basis
obs = list(DndTokenizer(sample))
self.assertEqual(len(obs), len(exp))
for i, j in zip(obs, exp):
self.assertEqual(i, j)
# try it all in one go
self.assertEqual(list(DndTokenizer(sample)), exp)
def test_nonames(self):
"""DndTokenizer should work as expected on trees with no names"""
exp = ["(", "(", ",", ")", ",", "(", ",", ")", ")", ";"]
obs = list(DndTokenizer(no_names))
self.assertEqual(obs, exp)
def test_missing_tip_name(self):
"""DndTokenizer should work as expected on trees with a missing name"""
exp = ["(", "(", "a", ",", "b", ")", ",", "(", "c", ",", ")", ")", ";"]
obs = list(DndTokenizer(missing_tip_name))
self.assertEqual(obs, exp)
def test_minimal(self):
"""DndTokenizer should work as expected a minimal tree without names"""
exp = ["(", ")", ";"]
obs = list(DndTokenizer(minimal))
self.assertEqual(obs, exp)
class DndParserTests(TestCase):
"""Tests of the DndParser factory function."""
def test_nonames(self):
"""DndParser should produce the correct tree when there are no names"""
obs = DndParser(no_names)
exp = PhyloNode()
exp.append(PhyloNode())
exp.append(PhyloNode())
exp.children[0].append(PhyloNode())
exp.children[0].append(PhyloNode())
exp.children[1].append(PhyloNode())
exp.children[1].append(PhyloNode())
self.assertEqual(str(obs), str(exp))
def test_minimal(self):
"""DndParser should produce the correct minimal tree"""
obs = DndParser(minimal)
exp = PhyloNode()
exp.append(PhyloNode())
self.assertEqual(str(obs), str(exp))
def test_missing_tip_name(self):
"""DndParser should produce the correct tree when missing a name"""
obs = DndParser(missing_tip_name)
exp = PhyloNode()
exp.append(PhyloNode())
exp.append(PhyloNode())
exp.children[0].append(PhyloNode(name="a"))
exp.children[0].append(PhyloNode(name="b"))
exp.children[1].append(PhyloNode(name="c"))
exp.children[1].append(PhyloNode())
self.assertEqual(str(obs), str(exp))
def test_gsingle(self):
"""DndParser should produce a single-child PhyloNode on minimal data"""
t = DndParser(single)
self.assertEqual(len(t), 1)
child = t[0]
self.assertEqual(child.name, "abc")
self.assertEqual(child.length, 3)
self.assertEqual(str(t), "(abc:3.0);")
def test_gdouble(self):
"""DndParser should produce a double-child PhyloNode from data"""
t = DndParser(double)
self.assertEqual(len(t), 2)
self.assertEqual(str(t), "(abc:3.0,def:4.0);")
def test_gonenest(self):
"""DndParser should work correctly with nested data"""
t = DndParser(onenest)
self.assertEqual(len(t), 2)
self.assertEqual(len(t[0]), 0) # first child is terminal
self.assertEqual(len(t[1]), 2) # second child has two children
self.assertEqual(str(t), "(abc:3.0,(def:4.0,ghi:5.0):6.0);")
def test_gnodedata(self):
"""DndParser should assign name to internal nodes correctly"""
t = DndParser(nodedata)
self.assertEqual(len(t), 2)
self.assertEqual(len(t[0]), 0) # first child is terminal
self.assertEqual(len(t[1]), 2) # second child has two children
self.assertEqual(str(t), "(abc:3.0,(def:4.0,ghi:5.0)jkl:6.0);")
info_dict = {}
for node in t.traverse():
info_dict[node.name] = node.length
self.assertEqual(info_dict["abc"], 3.0)
self.assertEqual(info_dict["def"], 4.0)
self.assertEqual(info_dict["ghi"], 5.0)
self.assertEqual(info_dict["jkl"], 6.0)
def test_data(self):
"""DndParser should work as expected on real data"""
t = DndParser(sample)
self.assertEqual(
str(t),
"((xyz:0.28124,(def:0.24498,mno:0.03627):0.1771):0.0487,abc:0.05925,(ghi:0.06914,jkl:0.13776):0.09853);",
)
tdata = DndParser(node_data_sample, unescape_name=True)
self.assertEqual(
str(tdata),
"((xyz:0.28124,(def:0.24498,mno:0.03627)A:0.1771)B:0.0487,abc:0.05925,(ghi:0.06914,jkl:0.13776)C:0.09853);",
)
def test_gbad(self):
"""DndParser should fail if parens unbalanced"""
left = "((abc:3)"
right = "(abc:3))"
self.assertRaises(RecordError, DndParser, left)
self.assertRaises(RecordError, DndParser, right)
def test_DndParser(self):
"""DndParser tests"""
t_str = "(A_a,(B:1.0,C),'D_e':0.5)E;"
tree_unesc = DndParser(t_str, PhyloNode, unescape_name=True)
tree_esc = DndParser(t_str, PhyloNode, unescape_name=False)
self.assertEqual(tree_unesc.name, "E")
self.assertEqual(tree_unesc.children[0].name, "A a")
self.assertEqual(tree_unesc.children[1].children[0].name, "B")
self.assertEqual(tree_unesc.children[1].children[0].length, 1.0)
self.assertEqual(tree_unesc.children[1].children[1].name, "C")
self.assertEqual(tree_unesc.children[2].name, "D_e")
self.assertEqual(tree_unesc.children[2].length, 0.5)
self.assertEqual(tree_esc.name, "E")
self.assertEqual(tree_esc.children[0].name, "A_a")
self.assertEqual(tree_esc.children[1].children[0].name, "B")
self.assertEqual(tree_esc.children[1].children[0].length, 1.0)
self.assertEqual(tree_esc.children[1].children[1].name, "C")
self.assertEqual(tree_esc.children[2].name, "'D_e'")
self.assertEqual(tree_esc.children[2].length, 0.5)
reload_test = tree_esc.get_newick(with_distances=True, escape_name=False)
obs = DndParser(reload_test, unescape_name=False)
self.assertEqual(
obs.get_newick(with_distances=True),
tree_esc.get_newick(with_distances=True),
)
reload_test = tree_unesc.get_newick(with_distances=True, escape_name=False)
obs = DndParser(reload_test, unescape_name=False)
self.assertEqual(
obs.get_newick(with_distances=True),
tree_unesc.get_newick(with_distances=True),
)
class PhyloNodeTests(TestCase):
"""Check that PhyloNode works the way I think"""
def test_gops(self):
"""Basic PhyloNode operations should work as expected"""
p = PhyloNode()
self.assertEqual(str(p), ";")
p.name = "abc"
self.assertEqual(str(p), "abc;")
p.length = 3
self.assertEqual(str(p), "abc:3;") # don't suppress branch from root
q = PhyloNode()
p.append(q)
self.assertEqual(str(p), "()abc:3;")
r = PhyloNode()
q.append(r)
self.assertEqual(str(p), "(())abc:3;")
r.name = "xyz"
self.assertEqual(str(p), "((xyz))abc:3;")
q.length = 2
self.assertEqual(str(p), "((xyz):2)abc:3;")
def test_make_tree_simple():
from cogent3 import make_tree
tree = make_tree(treestring="(a:0.4,b:0.5,c:0.6)")
assert tree.get_node_matching_name("a").length == 0.4
assert tree.get_node_matching_name("b").length == 0.5
assert tree.get_node_matching_name("c").length == 0.6
def test_stores_nhx_data(DATA_DIR):
"""capture extended newick data into <node>.params['other']"""
with open(DATA_DIR / "nhx.tree") as path:
got = DndParser(path)
rodent = got.get_connecting_node("Mouse", "Rat")
assert set(rodent.params["other"]) == {
'&sCF="89.13"',
'sCF/sDF1/sDF2="89.13/5.49/5.38"',
'sCF_N="107.21"',
'sCF_N/sDF1_N/sDF2_N="107.21/6.63/6.49"',
'sDF1="5.49"',
'sDF1_N="6.63"',
'sDF2="5.38"',
'sDF2_N="6.49"',
'sN="120.33"',
}
def test_subtree_nhx_data(DATA_DIR):
"""capture extended newick data into <node>.params['other']"""
with open(DATA_DIR / "nhx.tree") as path:
tree = DndParser(path)
subtree = tree.get_sub_tree(["Seal", "Mouse", "Rat", "Platypus", "Opossum"])
rodent = subtree.get_connecting_node("Mouse", "Rat")
assert set(rodent.params["other"]) == {
'&sCF="89.13"',
'sCF/sDF1/sDF2="89.13/5.49/5.38"',
'sCF_N="107.21"',
'sCF_N/sDF1_N/sDF2_N="107.21/6.63/6.49"',
'sDF1="5.49"',
'sDF1_N="6.63"',
'sDF2="5.38"',
'sDF2_N="6.49"',
'sN="120.33"',
}
def test_make_tree_with_nhx(DATA_DIR):
"""capture extended newick data into <node>.params['other']"""
from cogent3 import make_tree
nwk = (
'(t1:0.1,(t2:0.2,t3:0.3):0.4[&sCF="81.73"],'
'((t4:0.5,t5:0.6):0.7[&sCF="50.68",sDF1="24.42"],'
't6:0.8):0.9[&sCF="77.1",sDF1="11.53"]);'
)
got = make_tree(nwk)
vert = got.get_connecting_node("t2", "t3")
assert set(vert.params["other"]) == {'&sCF="81.73"'}
vert = got.get_connecting_node("t4", "t5")
assert set(vert.params["other"]) == {'&sCF="50.68"', 'sDF1="24.42"'}
vert = got.get_connecting_node("t5", "t6")
assert set(vert.params["other"]) == {'&sCF="77.1"', 'sDF1="11.53"'}
|
