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
|
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import os
import tempfile
import pybedtools.test.tfuncs as tfuncs
import pybedtools
import gzip
setup = tfuncs.setup_module
teardown = tfuncs.teardown_module
def _make_temporary_gzip(bed_filename):
"""
Make a gzip file on the fly
:param bed_filename: Filename of bed file to gzip
:return: filename of gzipped file
"""
orig_suffix = pybedtools.settings.tempfile_suffix
pybedtools.settings.tempfile_suffix = '.gz'
gz_filename = pybedtools.BedTool._tmp()
pybedtools.settings.tempfile_suffix = orig_suffix
with gzip.open(gz_filename, 'wb') as out_:
with open(bed_filename, 'rb') as in_:
out_.writelines(in_)
return gz_filename
def test_gzipped_file_types_are_bed():
agz = _make_temporary_gzip(pybedtools.example_filename('a.bed'))
agz = pybedtools.BedTool(agz)
assert 'bed' == agz.file_type
def test_gzipped_files_can_be_intersected():
agz = _make_temporary_gzip(pybedtools.example_filename('a.bed'))
bgz = _make_temporary_gzip(pybedtools.example_filename('b.bed'))
agz = pybedtools.BedTool(agz)
bgz = pybedtools.BedTool(bgz)
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
assert a.intersect(b) == agz.intersect(bgz) == a.intersect(bgz) == agz.intersect(b)
def test_gzipped_files_are_iterable_as_normal():
agz = _make_temporary_gzip(pybedtools.example_filename('a.bed'))
agz = pybedtools.BedTool(agz)
a = pybedtools.example_bedtool('a.bed')
for i in agz:
print(i)
assert list(a) == list(agz)
def test_str_representation_of_gzipped_files_is_the_same_as_normal():
agz = _make_temporary_gzip(pybedtools.example_filename('a.bed'))
agz = pybedtools.BedTool(agz)
a = pybedtools.example_bedtool('a.bed')
assert str(a) == str(agz)
def test_head_of_gzipped_files_is_the_same_as_normal():
agz = _make_temporary_gzip(pybedtools.example_filename('a.bed'))
agz = pybedtools.BedTool(agz)
a = pybedtools.example_bedtool('a.bed')
assert agz.head() == a.head()
def test_gzipped_output():
_filename = pybedtools.example_filename('a.bed')
compressed_file = pybedtools.BedTool(_filename).saveas(compressed=True)
# Open gzipped file in text mode
with gzip.open(compressed_file.fn, 'rt') as gf:
uncompressed_content = gf.read()
with open(_filename) as f:
original_content = f.read()
assert original_content == uncompressed_content
def test_gzipping_is_default_when_extension_is_dot_gz():
_filename = pybedtools.example_filename('a.bed')
with open(_filename) as f:
expected_content = f.read()
__, temp_filename = tempfile.mkstemp(suffix='.gz')
try:
bedtool = pybedtools.BedTool(_filename)
bedtool.saveas(fn=temp_filename)
with gzip.open(temp_filename, 'rt') as gf:
# gzip will fail next line if file is not gzipped
actual_content = gf.read()
assert expected_content == actual_content
finally:
if os.path.isfile(temp_filename):
os.unlink(temp_filename)
def test_gzipping_can_be_turned_off_even_for_dot_gz():
_filename = pybedtools.example_filename('a.bed')
with open(_filename) as f:
expected_content = f.read()
__, temp_filename = tempfile.mkstemp(suffix='.gz')
try:
bedtool = pybedtools.BedTool(_filename)
bedtool.saveas(fn=temp_filename, compressed=False)
with open(temp_filename) as non_gz_f:
# actual content will be jumbled if non_gz_f is unset
actual_content = non_gz_f.read()
assert expected_content == actual_content
finally:
if os.path.isfile(temp_filename):
os.unlink(temp_filename)
|
