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_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_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_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_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_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_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),
)
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_minimal(self):
"""DndParser should produce the correct minimal tree"""
obs = DndParser(minimal)
exp = PhyloNode()
exp.append(PhyloNode())
self.assertEqual(str(obs), str(exp))