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
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
|
# Copyright 2001 by Brad Chapman. All rights reserved.
# Revisions copyright 2011-2013 by Peter Cock. All rights reserved.
# Copyright 2015-2017 by Kai Blin. 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.
"""Tests Bio.SeqFeature."""
import unittest
import warnings
from copy import deepcopy
from os import path
from Bio import BiopythonDeprecationWarning
from Bio import BiopythonParserWarning
from Bio import Seq
from Bio import SeqIO
from Bio import SeqRecord
from Bio.Data.CodonTable import TranslationError
from Bio.SeqFeature import AfterPosition
from Bio.SeqFeature import BeforePosition
from Bio.SeqFeature import BetweenPosition
from Bio.SeqFeature import CompoundLocation
from Bio.SeqFeature import ExactPosition
from Bio.SeqFeature import OneOfPosition
from Bio.SeqFeature import SeqFeature
from Bio.SeqFeature import SimpleLocation
from Bio.SeqFeature import UnknownPosition
from Bio.SeqFeature import WithinPosition
class TestReference(unittest.TestCase):
"""Tests for the SeqFeature.Reference class."""
def test_eq_identical(self):
"""Test two identical references eq() to True."""
testfile = path.join("GenBank", "origin_line.gb")
rec1 = SeqIO.read(testfile, "genbank")
rec2 = SeqIO.read(testfile, "genbank")
self.assertEqual(
rec1.annotations["references"][0], rec1.annotations["references"][0]
)
self.assertEqual(
rec1.annotations["references"][0], rec2.annotations["references"][0]
)
self.assertNotEqual(
rec1.annotations["references"][0], rec1.annotations["references"][1]
)
self.assertNotEqual(
rec1.annotations["references"][0], rec2.annotations["references"][1]
)
self.assertEqual(
rec1.annotations["references"][1], rec1.annotations["references"][1]
)
self.assertEqual(
rec1.annotations["references"][1], rec2.annotations["references"][1]
)
class TestSimpleLocation(unittest.TestCase):
"""Tests for the SeqFeature.SimpleLocation class."""
def test_offsets(self):
"""Test adding and subtracting integer offsets."""
loc1 = SimpleLocation(23, 42, -1)
loc2 = SimpleLocation(123, 142, -1)
self.assertEqual(loc1 + 100, loc2)
self.assertEqual(loc1, loc2 + (-100))
self.assertEqual(loc1, loc2 - 100)
self.assertEqual(loc1 + 50, loc2 - 50)
with self.assertRaises(TypeError):
loc1 + "Hello"
with self.assertRaises(TypeError):
loc1 - "Hello"
def test_eq_identical(self):
"""Test two identical locations are equal."""
loc1 = SimpleLocation(23, 42, 1)
loc2 = SimpleLocation(23, 42, 1)
self.assertEqual(loc1, loc2)
loc1 = SimpleLocation(23, 42, -1)
loc2 = SimpleLocation(23, 42, -1)
self.assertEqual(loc1, loc2)
loc1 = SimpleLocation(BeforePosition(23), AfterPosition(42), 1)
loc2 = SimpleLocation(23, 42, 1)
self.assertEqual(loc1, loc2)
loc1 = SimpleLocation(23, 42, 1, "foo", "bar")
loc2 = SimpleLocation(23, 42, 1, "foo", "bar")
self.assertEqual(loc1, loc2)
def test_eq_not_identical(self):
"""Test two different locations are not equal."""
loc1 = SimpleLocation(22, 42, 1)
loc2 = SimpleLocation(23, 42, 1)
self.assertNotEqual(loc1, loc2)
loc1 = SimpleLocation(23, 42, 1)
loc2 = SimpleLocation(23, 43, 1)
self.assertNotEqual(loc1, loc2)
loc1 = SimpleLocation(23, 42, 1)
loc2 = SimpleLocation(23, 42, -1)
self.assertNotEqual(loc1, loc2)
loc1 = SimpleLocation(23, 42, 1)
loc2 = (23, 42, 1)
self.assertNotEqual(loc1, loc2)
loc1 = SimpleLocation(23, 42, 1, "foo")
loc2 = SimpleLocation(23, 42, 1, "bar")
self.assertNotEqual(loc1, loc2)
loc1 = SimpleLocation(23, 42, 1, "foo", "bar")
loc2 = SimpleLocation(23, 42, 1, "foo", "baz")
self.assertNotEqual(loc1, loc2)
def test_start_before_end(self):
expected = "must be greater than or equal to start location"
with self.assertRaises(ValueError) as err:
SimpleLocation(42, 23, 1)
self.assertIn(expected, str(err.exception))
with self.assertRaises(ValueError) as err:
SimpleLocation(42, 0, 1)
self.assertIn(expected, str(err.exception))
with self.assertRaises(ValueError) as err:
SimpleLocation(BeforePosition(42), AfterPosition(23), -1)
self.assertIn(expected, str(err.exception))
with self.assertRaises(ValueError) as err:
SimpleLocation(42, AfterPosition(0), 1)
self.assertIn(expected, str(err.exception))
# Features with UnknownPositions should pass check
SimpleLocation(42, UnknownPosition())
SimpleLocation(UnknownPosition(), 42)
# Same start and end should pass check
SimpleLocation(42, 42)
class TestCompoundLocation(unittest.TestCase):
"""Tests for the SeqFeature.CompoundLocation class."""
def test_eq_identical(self):
"""Test two identical locations are equal."""
loc1 = SimpleLocation(12, 17, 1) + SimpleLocation(23, 42, 1)
loc2 = SimpleLocation(12, 17, 1) + SimpleLocation(23, 42, 1)
self.assertEqual(loc1, loc2)
loc1 = SimpleLocation(12, 17, 1) + SimpleLocation(23, 42, 1)
loc2 = CompoundLocation([SimpleLocation(12, 17, 1), SimpleLocation(23, 42, 1)])
self.assertEqual(loc1, loc2)
def test_eq_not_identical(self):
"""Test two different locations are not equal."""
loc1 = SimpleLocation(12, 17, 1) + SimpleLocation(23, 42, 1)
loc2 = (
SimpleLocation(12, 17, 1)
+ SimpleLocation(23, 42, 1)
+ SimpleLocation(50, 60, 1)
)
self.assertNotEqual(loc1, loc2)
loc1 = SimpleLocation(12, 17, 1) + SimpleLocation(23, 42, 1)
loc2 = SimpleLocation(12, 17, -1) + SimpleLocation(23, 42, -1)
self.assertNotEqual(loc1, loc2)
loc1 = CompoundLocation([SimpleLocation(12, 17, 1), SimpleLocation(23, 42, 1)])
loc2 = CompoundLocation(
[SimpleLocation(12, 17, 1), SimpleLocation(23, 42, 1)], "order"
)
self.assertNotEqual(loc1, loc2)
loc1 = SimpleLocation(12, 17, 1) + SimpleLocation(23, 42, 1)
loc2 = 5
self.assertNotEqual(loc1, loc2)
class TestSeqFeature(unittest.TestCase):
"""Tests for the SeqFeature.SeqFeature class."""
def test_eq_identical(self):
f1 = SeqFeature(
type="CDS",
location=SimpleLocation(0, 182, 1),
qualifiers={
"product": ["interferon beta, fibroblast"],
},
)
f2 = deepcopy(f1)
self.assertEqual(f1, f2)
def test_translation_checks_cds(self):
"""Test that a CDS feature is subject to respective checks."""
seq = Seq.Seq("GGTTACACTTACCGATAATGTCTCTGATGA")
f = SeqFeature(SimpleLocation(0, 30), type="CDS")
f.qualifiers["transl_table"] = [11]
with self.assertRaises(TranslationError):
f.translate(seq)
def test_location_aliases(self):
f = SeqFeature(None, type="CDS")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("ignore", BiopythonDeprecationWarning)
with self.assertRaisesRegex(
AttributeError,
# "The .strand alias is only available when .location is defined.",
"'NoneType' object has no attribute 'strand'",
):
f.strand
self.assertEqual(None, f.ref)
self.assertEqual(None, f.ref_db)
class TestLocations(unittest.TestCase):
def test_fuzzy(self):
"""Test fuzzy representations."""
# check the positions alone
exact_pos = ExactPosition(5)
within_pos_s = WithinPosition(10, left=10, right=13)
within_pos_e = WithinPosition(13, left=10, right=13)
between_pos_e = BetweenPosition(24, left=20, right=24)
before_pos = BeforePosition(15)
after_pos = AfterPosition(40)
self.assertEqual(int(within_pos_s), 10)
self.assertEqual(str(within_pos_s), "(10.13)")
self.assertEqual(int(within_pos_e), 13)
self.assertEqual(str(within_pos_e), "(10.13)")
self.assertEqual(int(between_pos_e), 24)
self.assertEqual(str(between_pos_e), "(20^24)")
self.assertEqual(str(before_pos), "<15")
self.assertEqual(str(after_pos), ">40")
# put these into Locations
location1 = SimpleLocation(exact_pos, within_pos_e)
location2 = SimpleLocation(before_pos, between_pos_e)
location3 = SimpleLocation(within_pos_s, after_pos)
self.assertEqual(str(location1), "[5:(10.13)]")
self.assertEqual(str(location1.start), "5")
self.assertEqual(str(location1.end), "(10.13)")
self.assertEqual(str(location2), "[<15:(20^24)]")
self.assertEqual(str(location2.start), "<15")
self.assertEqual(str(location2.end), "(20^24)")
self.assertEqual(str(location3), "[(10.13):>40]")
self.assertEqual(str(location3.start), "(10.13)")
self.assertEqual(str(location3.end), ">40")
# --- test non-fuzzy representations
self.assertEqual(int(location1.start), 5)
self.assertEqual(int(location1.end), 13)
self.assertEqual(int(location2.start), 15)
self.assertEqual(int(location2.end), 24)
self.assertEqual(int(location3.start), 10)
self.assertEqual(int(location3.end), 40)
class TestPositions(unittest.TestCase):
def test_pickle(self):
"""Test pickle behaviour of position instances."""
# setup
import pickle
within_pos = WithinPosition(10, left=10, right=13)
between_pos = BetweenPosition(24, left=20, right=24)
oneof_pos = OneOfPosition(1888, [ExactPosition(1888), ExactPosition(1901)])
# test __getnewargs__
self.assertEqual(within_pos.__getnewargs__(), (10, 10, 13))
self.assertEqual(between_pos.__getnewargs__(), (24, 20, 24))
self.assertEqual(
oneof_pos.__getnewargs__(),
(1888, [ExactPosition(1888), ExactPosition(1901)]),
)
# test pickle behaviour
within_pos2 = pickle.loads(pickle.dumps(within_pos))
between_pos2 = pickle.loads(pickle.dumps(between_pos))
oneof_pos2 = pickle.loads(pickle.dumps(oneof_pos))
self.assertEqual(within_pos, within_pos2)
self.assertEqual(between_pos, between_pos2)
self.assertEqual(oneof_pos, oneof_pos2)
self.assertEqual(within_pos._left, within_pos2._left)
self.assertEqual(within_pos._right, within_pos2._right)
self.assertEqual(between_pos._left, between_pos2._left)
self.assertEqual(between_pos._right, between_pos2._right)
self.assertEqual(oneof_pos.position_choices, oneof_pos2.position_choices)
class TestExtract(unittest.TestCase):
def test_reference_in_location_record(self):
"""Test location with reference to another record."""
parent_record = SeqRecord.SeqRecord(seq=Seq.Seq("actg"))
another_record = SeqRecord.SeqRecord(seq=Seq.Seq("gtcagctac"))
location = SimpleLocation(5, 8, ref="ANOTHER.7")
with self.assertRaisesRegex(
ValueError,
r"Feature references another sequence \(ANOTHER\.7\), references mandatory",
):
location.extract(parent_record)
with self.assertRaisesRegex(
ValueError,
r"Feature references another sequence \(ANOTHER\.7\), not found in references",
):
location.extract(parent_record, references={"SOMEOTHER.2": another_record})
record = location.extract(
parent_record, references={"ANOTHER.7": another_record}
)
self.assertEqual(type(record), SeqRecord.SeqRecord)
self.assertEqual(record.seq, "cta")
def test_reference_in_location_sequence(self):
"""Test location with reference to another sequence."""
parent_sequence = Seq.Seq("actg")
another_sequence = Seq.Seq("gtcagctac")
location = SimpleLocation(5, 8, ref="ANOTHER.7")
sequence = location.extract(
parent_sequence, references={"ANOTHER.7": another_sequence}
)
self.assertEqual(type(sequence), Seq.Seq)
self.assertEqual(sequence, "cta")
def test_reference_in_compound_location_record(self):
"""Test compound location with reference to another record."""
parent_record = SeqRecord.SeqRecord(Seq.Seq("aaccaaccaaccaaccaa"))
another_record = SeqRecord.SeqRecord(Seq.Seq("ttggttggttggttggtt"))
location = SimpleLocation(2, 6) + SimpleLocation(5, 8, ref="ANOTHER.7")
with self.assertRaisesRegex(
ValueError,
r"Feature references another sequence \(ANOTHER\.7\), references mandatory",
):
location.extract(parent_record)
with self.assertRaisesRegex(
ValueError,
r"Feature references another sequence \(ANOTHER\.7\), not found in references",
):
location.extract(parent_record, references={"SOMEOTHER.2": another_record})
record = location.extract(
parent_record, references={"ANOTHER.7": another_record}
)
self.assertEqual(type(record), SeqRecord.SeqRecord)
self.assertEqual(record.seq, "ccaatgg")
def test_reference_in_compound_location_sequence(self):
"""Test compound location with reference to another sequence."""
parent_sequence = Seq.Seq("aaccaaccaaccaaccaa")
another_sequence = Seq.Seq("ttggttggttggttggtt")
location = SimpleLocation(2, 6) + SimpleLocation(5, 8, ref="ANOTHER.7")
sequence = location.extract(
parent_sequence, references={"ANOTHER.7": another_sequence}
)
self.assertEqual(type(sequence), Seq.Seq)
self.assertEqual(sequence, "ccaatgg")
def test_origin_spanning_location(self):
"""Test location spanning origin."""
# Regular origin-spanning sequence
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=BiopythonParserWarning)
self.assertEqual(
str(SimpleLocation.fromstring("4..2", 4, True)), "join{[3:4], [0:2]}"
)
self.assertEqual(
str(SimpleLocation.fromstring("complement(4..2)", 4, True)),
"join{[0:2](-), [3:4](-)}",
)
# Origin-spanning location containing the entire sequence
self.assertEqual(
str(SimpleLocation.fromstring("3..2", 4, True)), "join{[2:4], [0:2]}"
)
self.assertEqual(
str(SimpleLocation.fromstring("complement(3..2)", 4, True)),
"join{[0:2](-), [2:4](-)}",
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
