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
|
import os
import filecmp
import pytest
from pyfaidx import BedError, FetchError
from pyfaidx.cli import main
from tempfile import NamedTemporaryFile
path = os.path.dirname(__file__)
os.chdir(path)
@pytest.fixture
def remove_index():
yield
try:
os.remove('data/genes.fasta.fai')
except EnvironmentError:
pass # some tests may delete this file
def test_short_line_lengths(remove_index):
with pytest.raises(BedError):
main(['data/genes.fasta', '--bed', 'data/malformed.bed'])
def test_fetch_whole_file(remove_index):
main(['data/genes.fasta'])
def test_split_entry(remove_index):
main(['--split-files', 'data/genes.fasta', 'gi|557361099|gb|KF435150.1|'])
assert os.path.exists('gi557361099gbKF435150.1.fasta')
os.remove('gi557361099gbKF435150.1.fasta')
def test_fetch_error(remove_index):
with pytest.raises(FetchError):
main(['data/genes.fasta', 'gi|557361099|gb|KF435150.1|:1-1000'])
def test_key_warning(remove_index):
main(['data/genes.fasta', 'foo'])
def test_auto_strand(remove_index):
""" Test that --auto-strand produces the same output as --reverse --complement"""
with NamedTemporaryFile() as auto_strand:
with NamedTemporaryFile() as noto_strand:
main(['--auto-strand', '-o', auto_strand.name, 'data/genes.fasta', 'gi|557361099|gb|KF435150.1|:100-1'])
main(['--reverse', '--complement', '-o', noto_strand.name, 'data/genes.fasta', 'gi|557361099|gb|KF435150.1|:1-100'])
print(auto_strand.read())
print()
print(noto_strand.read())
assert filecmp.cmp(auto_strand.name, noto_strand.name)
def test_regexp(remove_index):
main(['data/genes.fasta', '-g', 'XR'])
def test_not_regexp(remove_index):
main(['data/genes.fasta', '-g', 'XR','-v'])
def test_not_regexp_multi(remove_index):
main(['data/genes.fasta', '-g', 'XR', '-g', 'XM', '-v'])
|
