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
|
#!/usr/bin/env python
# Copyright (c) 2006, The Regents of the University of California, through
# Lawrence Berkeley National Laboratory (subject to receipt of any required
# approvals from the U.S. Dept. of Energy). All rights reserved.
# This software is distributed under the new BSD Open Source License.
# <http://www.opensource.org/licenses/bsd-license.html>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# (1) Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# (2) Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and or other materials provided with the distribution.
#
# (3) Neither the name of the University of California, Lawrence Berkeley
# National Laboratory, U.S. Dept. of Energy nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import unittest
from io import StringIO
from weblogo.seq import protein_alphabet
from weblogo.seq_io import clustal_io, phylip_io, plain_io
from . import data_stream
class test_phylip_io(unittest.TestCase):
def test_read(self) -> None:
f = data_stream("phylip_test_1.phy")
seqs = phylip_io.read(f)
# print seqs
self.assertEqual(len(seqs), 10)
self.assertEqual(seqs[0].name, "Cow")
self.assertEqual(len(seqs[1]), 234)
f.close()
def test_iterseq(self) -> None:
f = data_stream("phylip_test_1.phy")
n = 0
for seq in phylip_io.iterseq(f):
n += 1
assert n == 10
f.close()
def test_parse_plain_fail(self) -> None:
# should fail with parse error
f = StringIO(plain_io.example)
self.assertRaises(ValueError, phylip_io.read, f)
def test_parse_phylip_test_2(self) -> None:
f = data_stream("phylip_test_2.phy")
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 6)
self.assertEqual(len(seqs[0]), 20)
self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
self.assertEqual(seqs[1].name, "Hesperorni")
f.close()
def test_parse_clustal_fail(self) -> None:
# should fail with parse error
f = StringIO(clustal_io.example)
self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet)
def test_parse_phylip_test_3(self) -> None:
f = data_stream("phylip_test_3.phy")
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 6)
self.assertEqual(len(seqs[0]), 20)
self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
self.assertEqual(seqs[1].name, "Hesperorni")
f.close()
def test_parse_phylip_test_4(self) -> None:
f = data_stream("phylip_test_4.phy")
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 6)
self.assertEqual(len(seqs[0]), 25)
self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGG")
self.assertEqual(seqs[2].name, "ddrasa")
f.close()
def test_parse_phylip_test_5(self) -> None:
f = data_stream("phylip_test_5.phy")
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 6)
self.assertEqual(len(seqs[0]), 50)
self.assertEqual(
str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGGGTGGTGGTGGGCGCCGGCCGTGTGG"
)
self.assertEqual(seqs[2].name, "ddrasa")
f.close()
def test_parse_wrong_phylip_codes_1(self) -> None:
f = data_stream("phylip_test_6.corrupt.phy")
self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet)
f.close()
def test_parse_wrong_phylip_codes_2(self) -> None:
f = data_stream("phylip_test_7.corrupt.phy")
self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet)
f.close()
def test_parse_phylip_dna(self) -> None:
f = data_stream("dna.phy")
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 10)
self.assertEqual(len(seqs[0]), 705)
self.assertEqual(str(seqs[1][0:10]), "ATGGCACACC")
self.assertEqual(seqs[2].name, "Chicken")
f.close()
if __name__ == "__main__":
unittest.main()
|
