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
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
|
"""Testing code for Restriction enzyme classes of Biopython.
"""
import os
import sys
import unittest
from Bio.Restriction import *
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
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 = [SimpleEnzyme, EnzymeComparison, RestrictionBatches]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
class SimpleEnzyme(unittest.TestCase):
"""Tests for dealing with basic enzymes using the Restriction package.
"""
def setUp(self):
base_seq = Seq("AAAA", IUPACAmbiguousDNA())
self.ecosite_seq = base_seq + Seq(EcoRI.site,
IUPACAmbiguousDNA()) + base_seq
def tearDown(self):
pass
def t_eco_cutting(self):
"""Test basic cutting with EcoRI.
"""
assert EcoRI.site == 'GAATTC'
assert EcoRI.is_blunt() == False
assert EcoRI.is_5overhang() == True
assert EcoRI.is_3overhang() == False
assert EcoRI.elucidate() == "G^AATT_C"
assert EcoRI.search(self.ecosite_seq) == [6]
parts = EcoRI.catalyse(self.ecosite_seq)
assert len(parts) == 2
assert parts[1].data == "AATTCAAAA"
parts = EcoRI.catalyze(self.ecosite_seq)
assert len(parts) == 2
def t_circular_sequences(self):
"""Deal with cutting circular sequences.
"""
parts = EcoRI.catalyse(self.ecosite_seq, linear = False)
assert len(parts) == 1
locations = EcoRI.search(parts[0], linear = False)
assert locations == [1]
class EnzymeComparison(unittest.TestCase):
"""Tests for comparing various enzymes.
"""
def setUp(self):
pass
def tearDown(self):
pass
def t_basic_isochizomers(self):
"""Test to be sure isochizomer and neoschizomers are as expected.
"""
assert Acc65I.isoschizomers() == [Asp718I, KpnI]
assert Acc65I.elucidate() == 'G^GTAC_C'
assert Asp718I.elucidate() == 'G^GTAC_C'
assert KpnI.elucidate() == 'G_GTAC^C'
def t_comparisons(self):
"""Comparison operators between iso and neoschizomers.
"""
assert Acc65I == Acc65I
assert Acc65I != KpnI
assert not(Acc65I == Asp718I)
assert not(Acc65I != Asp718I)
assert Acc65I != EcoRI
assert Acc65I >> KpnI
assert not(Acc65I >> Asp718I)
assert Acc65I % Asp718I
assert Acc65I % Acc65I
assert not(Acc65I % KpnI)
class RestrictionBatches(unittest.TestCase):
"""Tests for dealing with batches of restriction enzymes.
"""
def setUp(self):
pass
def tearDown(self):
pass
def t_creating_batch(self):
"""Creating and modifying a restriction batch.
"""
batch = RestrictionBatch([EcoRI])
batch.add(KpnI)
batch += EcoRV
assert len(batch) == 3
batch.get(EcoRV)
try:
batch.get(SmaI)
raise AssertionError("No error with non-existent enzyme.")
except ValueError:
pass
batch.remove(EcoRV)
assert len(batch) == 2
def t_batch_analysis(self):
"""Sequence analysis with a restriction batch.
"""
seq = Seq("AAAA" + EcoRV.site + "AAAA" + EcoRI.site + "AAAA",
IUPACAmbiguousDNA())
batch = RestrictionBatch([EcoRV, EcoRI])
hits = batch.search(seq)
assert hits[EcoRV] == [8] and hits[EcoRI] == [16]
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
|
