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
|
# Copyright (c) 2008-2015, Michigan State University
"""
Test `screed.open`.
"""
from __future__ import absolute_import
import os.path
import sys
import subprocess
from . import screed_tst_utils as utils
import screed
import screed.openscreed
def test_empty_open():
filename = utils.get_test_data('empty.fa')
assert len(list(screed.open(filename))) == 0
def test_open_maps_dash():
"""Test mapping of '-'."""
# pylint: disable=protected-access
filename = '-'
mapped = screed.openscreed._normalize_filename(filename)
assert '/dev/stdin' == mapped
def test_open_stdin():
"""Test feeding data through stdin.
Uses a subprocess with the data file directlyused as stdin."""
filename1 = utils.get_test_data('test.fa')
command = ["python3", "-c", "from __future__ import print_function;"
"import screed; print(list(screed.open('-')))"]
with open(filename1, 'rb') as data_file:
output = subprocess.Popen(command,
stdin=data_file, universal_newlines=True,
stdout=subprocess.PIPE).communicate()[0]
assert "'name': 'ENSMICT00000012722'" \
or "'name': u'ENSMICT00000012722'" in output, output
def test_simple_open():
filename = utils.get_test_data('test.fa')
n = -1
for n, record in enumerate(screed.open(filename, parse_description=True)):
assert record.name == 'ENSMICT00000012722'
break
assert n == 0, n
def test_simple_open_fq():
filename = utils.get_test_data('test.fastq')
n = -1
for n, record in enumerate(screed.open(filename)):
assert record.name == 'HWI-EAS_4_PE-FC20GCB:2:1:492:573/2'
break
assert n == 0
def test_gz_open():
filename1 = utils.get_test_data('test.fa')
filename2 = utils.get_test_data('test.fa.gz')
for n, (r1, r2) in enumerate(zip(screed.open(filename1),
screed.open(filename2))):
assert r1.name == r2.name
assert n > 0
def test_bz2_open():
filename1 = utils.get_test_data('test.fa')
filename2 = utils.get_test_data('test.fa.bz2')
for n, (r1, r2) in enumerate(zip(screed.open(filename1),
screed.open(filename2))):
assert r1.name == r2.name
assert n > 0
def test_gz_open_fastq():
filename1 = utils.get_test_data('test.fastq')
filename2 = utils.get_test_data('test.fastq.gz')
for n, (r1, r2) in enumerate(zip(screed.open(filename1),
screed.open(filename2))):
assert r1.name == r2.name
assert n > 0
def test_unknown_fileformat():
try:
screed.open(__file__)
except ValueError as err:
assert "unknown file format" in str(err)
|
