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
|
# Copyright 2014 by Melissa Gymrek <mgymrek@mit.edu>. 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.
import os
import shutil
import unittest
import warnings
from Bio import MissingExternalDependencyError
from Bio import BiopythonDeprecationWarning
with warnings.catch_warnings():
warnings.simplefilter("ignore", BiopythonDeprecationWarning)
from Bio.PopGen.SimCoal.Controller import FastSimCoalController
# Tests fastsimcoal related code. Note: this case requires fastsimcoal 2.51
found = False
for path in os.environ['PATH'].split(os.pathsep):
try:
for filename in os.listdir(path):
if filename == "fsc252" \
or (filename.lower() == "fsc252.exe"):
found = True
fastsimcoal_dir = path
except os.error:
pass # Path doesn't exist - correct to pass
if not found:
raise MissingExternalDependencyError(
"Install fastsimcoal if you want to use "
"Bio.PopGen.SimCoal.Controller.FastSimCoalController.")
class AppTest(unittest.TestCase):
"""Tests fastsimcoal execution via biopython.
"""
def setUp(self):
self.tidy()
def tearDown(self):
self.tidy()
def tidy(self):
if not os.path.isdir(os.path.join('PopGen', 'simple')):
# Unit test must have failed to invoke fastsimcoal251,
# and thus it never created the directory.
return
shutil.rmtree(os.path.join('PopGen', 'simple'))
def test_fastsimcoal(self):
"""Test fastsimcoal execution.
"""
ctrl = FastSimCoalController(fastsimcoal_dir=fastsimcoal_dir)
ctrl.run_fastsimcoal('simple.par', 50, par_dir='PopGen')
assert os.path.isdir(os.path.join('PopGen', 'simple')), \
"Output directory not created!"
assert(len(os.listdir(os.path.join('PopGen', 'simple'))) == 52)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
