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
|
#!/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 nucleic_alphabet, protein_alphabet, rna_alphabet
from weblogo.seq_io import clustal_io, fasta_io, stockholm_io
from . import data_stream
class test_stockholm_io(unittest.TestCase):
def test_parse1(self) -> None:
with data_stream("pfam.txt") as f:
seqs = stockholm_io.read(f)
# self.assertEqual(len(seqs), 7)
self.assertEqual(seqs[1].name, "O61132/1-232")
self.assertEqual(len(seqs[1]), 265)
def test_parse2(self) -> None:
f = StringIO(stockholm_io.example)
seqs = stockholm_io.read(f)
self.assertEqual(len(seqs), 5)
self.assertEqual(seqs[1].name, "O83071/259-312")
self.assertEqual(len(seqs[1]), 43)
def test_iterseq(self) -> None:
with data_stream("pfam.txt") as f:
for seq in stockholm_io.iterseq(f):
pass
# 12345678901234567890123456789012345678901234567890
# 12*50 +6 = 606
# QYVTVFYGVPAWRNATIPLFCATKNR.......DTWGTTQCLPDNDDYSE
def test_parse3(self) -> None:
with data_stream("pfam_example.txt") as f:
seqs = stockholm_io.read(f)
self.assertEqual(len(seqs), 24)
self.assertEqual(seqs[5].name, "ENV_HV2BE/24-510")
self.assertEqual(len(seqs[1]), 606)
self.assertEqual(str(seqs[0][-6:]), "TSRNKR")
def test_parse_error(self) -> None:
"""Wrong alphabet should throw a parsing error"""
f = StringIO(stockholm_io.example)
self.assertRaises(ValueError, clustal_io.read, f, nucleic_alphabet)
def test_parse_fasta_fail(self) -> None:
# should fail with parse error
f = StringIO(stockholm_io.example)
self.assertRaises(ValueError, stockholm_io.read, f, rna_alphabet)
def test_parse_alphabet_fail(self) -> None:
# should fail with parse error
f = StringIO(fasta_io.example)
self.assertRaises(ValueError, stockholm_io.read, f, protein_alphabet)
def test_parse_fasta_fail2(self) -> None:
# should fail with parse error
with data_stream("globin.fa") as f:
self.assertRaises(ValueError, stockholm_io.read, f)
def test_parse_fail(self) -> None:
# should fail with parse error
examples = (StringIO(clustal_io.example),)
for f in examples:
self.assertRaises(ValueError, stockholm_io.read, f)
if __name__ == "__main__":
unittest.main()
|
