1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
|
#!/usr/bin/env python
"""Unit tests for tree parsers.
"""
from cogent.parse.tree import DndParser, DndTokenizer, RecordError
from cogent.core.tree import PhyloNode
from cogent.util.unit_test import TestCase, main
#from cogent.parse.newick import parse_string, TreeParseError as RecordError
#def DndParser(data, NodeClass=PhyloNode, unescape_name=True):
# if not unescape_name:
# raise NotImplementedError
# def constructor(children, name, attribs):
# return NodeClass(Children = list(children or []), Name=name, Params=attribs)
# return parse_string(data, constructor)
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Rob Knight", "Peter Maxwell", "Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
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.getNewick(with_distances=True, \
escape_name=False)
obs = DndParser(reload_test, unescape_name=False)
self.assertEqual(obs.getNewick(with_distances=True), \
tree_esc.getNewick(with_distances=True))
reload_test = tree_unesc.getNewick(with_distances=True, \
escape_name=False)
obs = DndParser(reload_test, unescape_name=False)
self.assertEqual(obs.getNewick(with_distances=True), \
tree_unesc.getNewick(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;')
if __name__ == '__main__':
main()
|
