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
|
# Copyright 2006 by Tiago Antao <tiagoantao@gmail.com>. 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 commands
import os
import shutil
import sys
import tempfile
import unittest
from Bio.PopGen import GenePop
from Bio.PopGen import FDist
from Bio.PopGen.FDist.Utils import convert_genepop_to_fdist
#Tests fdist related code. Note: this case doesn't require fdist
#test_PopGen_FDist tests code that requires fdist
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests.
"""
test_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 't_'
tests = [RecordTest, ParserTest, ConversionTest]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
class RecordTest(unittest.TestCase):
def t_record_basic(self):
"""Basic test on Record
"""
r = FDist.Record()
assert type(r.data_org) == int
assert type(r.num_pops) == int
assert type(r.num_loci) == int
assert type(r.loci_data) == list
class ParserTest(unittest.TestCase):
def setUp(self):
files = ["fdist1"]
self.handles = []
for filename in files:
self.handles.append(open(os.path.join("PopGen", filename)))
self.pops_loci = [
(3, 4)
]
self.num_markers = [
[2, 3, 4, 2]
]
#format is locus, pop, position, value
self.test_pos = [
[
(0, 0, 0, 5),
(3, 2, 0, 5)
]
]
def tearDown(self):
for handle in self.handles:
handle.close()
def t_record_parser(self):
"""Basic operation of the Record Parser.
"""
parser = FDist.RecordParser()
for index in range(len(self.handles)):
handle = self.handles[index]
rec = parser.parse(handle)
assert isinstance(rec, FDist.Record)
assert rec.data_org == 0 #We don't support any other
assert rec.num_pops, rec.num_loci == self.pops_loci[index]
for i in range(len(self.num_markers[index])):
assert rec.loci_data[i][0] == \
self.num_markers[index][i]
for i in range(len(self.test_pos[index])):
my_test_pos = self.test_pos[index]
for test in my_test_pos:
locus, pop, pos, value = test
assert(rec.loci_data[locus][1][pop][pos] == value)
class ConversionTest(unittest.TestCase):
def setUp(self):
files = ["c2line.gen"]
self.handles = []
for filename in files:
self.handles.append(open(os.path.join("PopGen", filename)))
def t_convert(self):
"""Basic conversion test.
"""
for i in range(len(self.handles)):
gp_rec = GenePop.parse(self.handles[i])
fd_rec = convert_genepop_to_fdist(gp_rec)
assert(fd_rec.num_loci == 3)
assert(fd_rec.num_pops == 3)
def tearDown(self):
for handle in self.handles:
handle.close()
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
|
