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
|
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for Bio.File module."""
import os.path
import shutil
import tempfile
import unittest
from io import StringIO
from Bio import bgzf
from Bio import File
class RandomAccess(unittest.TestCase):
"""Random access tests."""
def test_plain(self):
"""Test plain text file."""
with File._open_for_random_access("Quality/example.fastq") as handle:
self.assertIn("r", handle.mode)
self.assertIn("b", handle.mode)
def test_bgzf(self):
"""Test BGZF compressed file."""
with File._open_for_random_access("Quality/example.fastq.bgz") as handle:
self.assertIsInstance(handle, bgzf.BgzfReader)
def test_gzip(self):
"""Test gzip compressed file."""
self.assertRaises(
ValueError, File._open_for_random_access, "Quality/example.fastq.gz"
)
class AsHandleTestCase(unittest.TestCase):
"""Tests for as_handle function."""
def setUp(self):
"""Initialise temporary directory."""
# Create a directory to work in
self.temp_dir = tempfile.mkdtemp(prefix="biopython-test")
def tearDown(self):
"""Remove temporary directory."""
shutil.rmtree(self.temp_dir)
def _path(self, *args):
return os.path.join(self.temp_dir, *args)
def test_handle(self):
"""Test as_handle with a file-like object argument."""
p = self._path("test_file.fasta")
with open(p, "wb") as fp:
with File.as_handle(fp) as handle:
self.assertEqual(
fp,
handle,
"as_handle should "
"return argument when given a "
"file-like object",
)
self.assertFalse(handle.closed)
self.assertFalse(
handle.closed,
"Exiting as_handle given a file-like object "
"should not close the file",
)
def test_string_path(self):
"""Test as_handle with a string path argument."""
p = self._path("test_file.fasta")
mode = "wb"
with File.as_handle(p, mode=mode) as handle:
self.assertEqual(p, handle.name)
self.assertEqual(mode, handle.mode)
self.assertFalse(handle.closed)
self.assertTrue(handle.closed)
def test_path_object(self):
"""Test as_handle with a pathlib.Path object."""
from pathlib import Path
p = Path(self._path("test_file.fasta"))
mode = "wb"
with File.as_handle(p, mode=mode) as handle:
self.assertEqual(str(p.absolute()), handle.name)
self.assertEqual(mode, handle.mode)
self.assertFalse(handle.closed)
self.assertTrue(handle.closed)
def test_custom_path_like_object(self):
"""Test as_handle with a custom path-like object."""
class CustomPathLike:
def __init__(self, path):
self.path = path
def __fspath__(self):
return self.path
p = CustomPathLike(self._path("test_file.fasta"))
mode = "wb"
with File.as_handle(p, mode=mode) as handle:
self.assertEqual(p.path, handle.name)
self.assertEqual(mode, handle.mode)
self.assertFalse(handle.closed)
self.assertTrue(handle.closed)
def test_stringio(self):
"""Testing passing StringIO handles."""
s = StringIO()
with File.as_handle(s) as handle:
self.assertIs(s, handle)
class BaseClassTests(unittest.TestCase):
"""Tests for _IndexedSeqFileProxy base class."""
def test_instance_exception(self):
self.assertRaises(TypeError, File._IndexedSeqFileProxy)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
