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
|
# Copyright 2019 Damien Goutte-Gattat. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Tests for the SeqIO SnapGene module."""
import datetime
import unittest
from io import BytesIO
from Bio import SeqIO
from Bio.SeqFeature import CompoundLocation
class TestSnapGene(unittest.TestCase):
sample_data = {
"sample-d": {
"file": "SnapGene/sample-d.dna",
"name": "Sample",
"id": "Sample",
"description": "Sample Sequence D",
"length": 1000,
"topology": "linear",
"date": datetime.datetime(2021, 7, 7, 0, 0),
"features": [
{
"type": "misc_binding",
"start": 499,
"end": 700,
"strand": 1,
"label": ["FeatureB"],
"note": ["Sample feature B"],
},
{
"type": "promoter",
"start": 49,
"end": 150,
"strand": 1,
"label": ["FeatureA"],
"note": ["Sample feature A"],
},
{
"type": "misc_feature",
"start": 700,
"end": 720,
"strand": 1,
"label": ["FeatureC"],
"note": [
"Sample feature C, with explicit label",
"Another note for sample feature C",
],
},
{
"type": "misc_feature",
"start": 720,
"end": 740,
"strand": 1,
"label": ["SampleFeatureD"],
"note": [
"Sample feature D, with a label different from the feature name"
],
"name": "FeatureD",
},
],
},
"sample-e": {
"file": "SnapGene/sample-e.dna",
"name": "Sample",
"id": "Sample",
"description": "Sample Sequence E",
"length": 1000,
"date": datetime.datetime(2019, 8, 3, 0, 0),
"topology": "circular",
"features": [
{
"type": "terminator",
"start": 399,
"end": 750,
"strand": -1,
"label": ["FeatureB"],
},
{
"type": "rep_origin",
"start": 160,
"end": 241,
"strand": 1,
"label": ["FeatureA"],
},
],
},
"sample-f": {
"file": "SnapGene/sample-f.dna",
"name": "Sample",
"id": "Sample",
"description": "Sample Sequence F",
"length": 1000,
"date": datetime.datetime(2023, 1, 22, 0, 0),
"topology": "circular",
"features": [
{
"type": "terminator",
"start": 399,
"end": 724,
"strand": -1,
"label": ["FeatureB"],
"note": ["An example of a reverse-strand split feature"],
"parts": ["1:subfeature1;3:subfeature3"],
"segments": [
{"start": 634, "end": 724},
{"start": 516, "end": 634},
{"start": 399, "end": 499},
],
},
{
"type": "rep_origin",
"start": 160,
"end": 241,
"strand": 1,
"label": ["FeatureA"],
"note": ["An example of a split feature"],
"parts": ["2:subfeature2"],
"segments": [
{"start": 160, "end": 180},
{"start": 187, "end": 207},
{"start": 214, "end": 241},
],
},
{
"type": "primer_bind",
"start": 751,
"end": 776,
"strand": 1,
"label": ["Primer 1"],
},
],
},
"pFA-KanMX4": {
"file": "SnapGene/pFA-KanMX4.dna",
"name": "<unknown name>",
"id": "<unknown id>",
"description": "<unknown description>",
"length": 3941,
"date": datetime.datetime(2020, 7, 30, 0, 0),
"topology": "circular",
"features": [
{
"type": "promoter",
"start": 0,
"end": 3941,
"strand": 1,
"label": ["SP6 promoter"],
},
{
"type": "promoter",
"start": 1578,
"end": 1597,
"strand": -1,
"label": ["T7 promoter"],
},
{
"type": "promoter",
"start": 3474,
"end": 3579,
"strand": -1,
"label": ["AmpR promoter"],
},
{
"type": "terminator",
"start": 1273,
"end": 1471,
"strand": 1,
"label": ["TEF terminator"],
},
{
"type": "promoter",
"start": 114,
"end": 458,
"strand": 1,
"label": ["TEF promoter"],
},
{
"type": "rep_origin",
"start": 1854,
"end": 2443,
"strand": -1,
"label": ["ori"],
},
{
"type": "CDS",
"start": 458,
"end": 1268,
"strand": 1,
"label": ["KanR"],
},
{
"type": "CDS",
"start": 2613,
"end": 3474,
"strand": -1,
"label": ["AmpR"],
"parts": ["1:signal sequence"],
"segments": [
{"start": 3405, "end": 3474},
{"start": 2613, "end": 3405},
],
},
{
"type": "gene",
"start": 114,
"end": 1471,
"strand": 1,
"label": ["kanMX"],
},
],
},
}
def _check_multivalued_qualifier(self, qualifier, expected, actual):
if qualifier in expected:
for value in expected[qualifier]:
self.assertIn(value, actual.qualifiers[qualifier])
def _check_feature_segments(self, segments, feature):
self.assertIsInstance(feature.location, CompoundLocation)
self.assertEqual(len(segments), len(feature.location.parts))
for i in range(len(segments)):
segment = segments[i]
location = feature.location.parts[i]
self.assertEqual(segment["start"], location.start)
self.assertEqual(segment["end"], location.end)
def test_read(self):
"""Read sample files."""
for sample in self.sample_data.values():
record = SeqIO.read(sample["file"], "snapgene")
self.assertEqual(sample["name"], record.name)
self.assertEqual(sample["id"], record.id)
self.assertEqual(sample["description"], record.description)
self.assertEqual(sample["length"], len(record))
self.assertEqual(sample["date"], record.annotations["date"])
self.assertEqual(sample["topology"], record.annotations["topology"])
self.assertEqual(len(sample["features"]), len(record.features))
for i in range(len(sample["features"])):
exp_feat = sample["features"][i]
read_feat = record.features[i]
self.assertEqual(exp_feat["type"], read_feat.type)
self.assertEqual(exp_feat["start"], read_feat.location.start)
self.assertEqual(exp_feat["end"], read_feat.location.end)
self.assertEqual(exp_feat["strand"], read_feat.location.strand)
self._check_multivalued_qualifier("label", exp_feat, read_feat)
self._check_multivalued_qualifier("note", exp_feat, read_feat)
self._check_multivalued_qualifier("parts", exp_feat, read_feat)
if "name" in exp_feat:
self.assertEqual(exp_feat["name"], read_feat.qualifiers["name"][0])
else:
self.assertTrue("name" not in read_feat.qualifiers)
if "segments" in exp_feat:
self._check_feature_segments(exp_feat["segments"], read_feat)
class TestCorruptedSnapGene(unittest.TestCase):
def setUp(self):
with open("SnapGene/sample-d.dna", "rb") as f:
self.buffer = f.read()
def munge_buffer(self, position, value):
mod_buffer = bytearray(self.buffer)
if isinstance(value, list):
mod_buffer[position : position + len(value) - 1] = value
else:
mod_buffer[position] = value
return BytesIO(mod_buffer)
def test_invalid_cookie(self):
"""Read a file with missing or invalid cookie packet."""
# Remove the first packet
h = BytesIO(self.buffer[19:])
with self.assertRaisesRegex(
ValueError, "The file does not start with a SnapGene cookie packet"
):
SeqIO.read(h, "snapgene")
h.close()
# Keep the first packet but destroy the magic cookie
h = self.munge_buffer(5, [0x4B, 0x41, 0x42, 0x4F, 0x4F, 0x4D])
with self.assertRaisesRegex(
ValueError, "The file is not a valid SnapGene file"
):
SeqIO.read(h, "snapgene")
h.close()
def test_missing_dna(self):
"""Read a file without a DNA packet."""
# Simulate a missing DNA packet by changing the tag byte to an
# unknown packet type, so that the parser will skip the packet.
h = self.munge_buffer(19, 0x80)
with self.assertRaisesRegex(ValueError, "No DNA packet in file"):
SeqIO.read(h, "snapgene")
h.close()
def test_extra_dna(self):
"""Read a file with supernumerary DNA packet."""
# Fabricate a file with a duplicated DNA packet
buf = bytearray(self.buffer)
buf.extend(self.buffer[19:1025]) # Append duplicated DNA packet
h = BytesIO(buf)
with self.assertRaisesRegex(
ValueError, "The file contains more than one DNA packet"
):
SeqIO.read(h, "snapgene")
h.close()
def test_truncated_packet(self):
"""Read a file with incomplete packet."""
# Truncate before the end of the length bytes
h = BytesIO(self.buffer[3:])
with self.assertRaisesRegex(ValueError, "Unexpected end of packet"):
SeqIO.read(h, "snapgene")
h.close()
# Truncate before the end of the data
h = BytesIO(self.buffer[10:])
with self.assertRaisesRegex(ValueError, "Unexpected end of packet"):
SeqIO.read(h, "snapgene")
h.close()
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
