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
|
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import unittest
import numpy.testing as npt
import numpy as np
from skbio import Sequence, DNA, RNA
from skbio.io.format._base import (_decode_qual_to_phred,
_encode_phred_to_qual, _get_nth_sequence,
_parse_fasta_like_header,
_format_fasta_like_records)
class PhredDecoderTests(unittest.TestCase):
def test_missing_variant_and_phred_offset(self):
with self.assertRaises(ValueError) as cm:
_decode_qual_to_phred('abcd')
self.assertIn('`variant`', str(cm.exception))
self.assertIn('`phred_offset`', str(cm.exception))
self.assertIn('decode', str(cm.exception))
def test_variant_and_phred_offset_provided(self):
with self.assertRaises(ValueError) as cm:
_decode_qual_to_phred('abcd', variant='sanger', phred_offset=64)
self.assertIn('both', str(cm.exception))
self.assertIn('`variant`', str(cm.exception))
self.assertIn('`phred_offset`', str(cm.exception))
def test_solexa_variant(self):
with self.assertRaises(ValueError) as cm:
_decode_qual_to_phred('abcd', variant='solexa')
self.assertIn('719', str(cm.exception))
def test_unrecognized_variant(self):
with self.assertRaises(ValueError) as cm:
_decode_qual_to_phred('abcd', variant='illumina')
self.assertIn('variant', str(cm.exception))
self.assertIn("'illumina'", str(cm.exception))
def test_empty_qual_str(self):
npt.assert_equal(_decode_qual_to_phred('', variant='sanger'),
np.array([], dtype=np.uint8))
def test_sanger_variant(self):
# test entire range of possible ascii chars for sanger
all_sanger_ascii = ('!"#$%&\'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOP'
'QRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~')
obs = _decode_qual_to_phred(all_sanger_ascii, variant='sanger')
npt.assert_equal(obs, np.arange(94))
with self.assertRaises(ValueError) as cm:
_decode_qual_to_phred('a b', variant='sanger')
self.assertIn('[0, 93]', str(cm.exception))
def test_illumina13_variant(self):
# test entire range of possible ascii chars for illumina1.3
all_illumina13_ascii = ('@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijk'
'lmnopqrstuvwxyz{|}~')
obs = _decode_qual_to_phred(all_illumina13_ascii,
variant='illumina1.3')
npt.assert_equal(obs, np.arange(63))
with self.assertRaises(ValueError) as cm:
_decode_qual_to_phred('a!b', variant='illumina1.3')
self.assertIn('[0, 62]', str(cm.exception))
def test_illumina18_variant(self):
# test entire range of possible ascii chars for illumina1.8
all_illumina18_ascii = ('!"#$%&\'()*+,-./0123456789:;<=>?@ABCDEFGHIJKL'
'MNOPQRSTUVWXYZ[\\]^_')
obs = _decode_qual_to_phred(all_illumina18_ascii,
variant='illumina1.8')
npt.assert_equal(obs, np.arange(63))
with self.assertRaises(ValueError) as cm:
_decode_qual_to_phred('AaB', variant='illumina1.8')
self.assertIn('[0, 62]', str(cm.exception))
def test_custom_phred_offset(self):
ascii_chars = '*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\'
obs = _decode_qual_to_phred(ascii_chars, phred_offset=42)
npt.assert_equal(obs, np.arange(51))
with self.assertRaises(ValueError) as cm:
_decode_qual_to_phred(ascii_chars, phred_offset=43)
self.assertIn('[0, 83]', str(cm.exception))
with self.assertRaises(ValueError) as cm:
_decode_qual_to_phred(ascii_chars, phred_offset=0)
self.assertIn('`phred_offset`', str(cm.exception))
self.assertIn('printable', str(cm.exception))
with self.assertRaises(ValueError) as cm:
_decode_qual_to_phred(ascii_chars, phred_offset=127)
self.assertIn('`phred_offset`', str(cm.exception))
self.assertIn('printable', str(cm.exception))
class PhredEncoderTests(unittest.TestCase):
def test_missing_variant_and_phred_offset(self):
with self.assertRaises(ValueError) as cm:
_encode_phred_to_qual([1, 2, 3])
self.assertIn('`variant`', str(cm.exception))
self.assertIn('`phred_offset`', str(cm.exception))
self.assertIn('encode', str(cm.exception))
def test_variant_and_phred_offset_provided(self):
with self.assertRaises(ValueError) as cm:
_encode_phred_to_qual([1, 2, 3], variant='sanger', phred_offset=64)
self.assertIn('both', str(cm.exception))
self.assertIn('`variant`', str(cm.exception))
self.assertIn('`phred_offset`', str(cm.exception))
def test_solexa_variant(self):
with self.assertRaises(ValueError) as cm:
_encode_phred_to_qual([1, 2, 3], variant='solexa')
self.assertIn('719', str(cm.exception))
def test_unrecognized_variant(self):
with self.assertRaises(ValueError) as cm:
_encode_phred_to_qual([1, 2, 3], variant='illumina')
self.assertIn('variant', str(cm.exception))
self.assertIn("'illumina'", str(cm.exception))
def test_no_phred_scores(self):
self.assertEqual(_encode_phred_to_qual([], variant='sanger'), '')
def test_sanger_variant(self):
# test entire range of possible ascii chars for sanger
all_sanger_ascii = ('!"#$%&\'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOP'
'QRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz{|}~')
obs = _encode_phred_to_qual(list(range(94)), variant='sanger')
self.assertEqual(obs, all_sanger_ascii)
with self.assertRaises(ValueError) as cm:
_encode_phred_to_qual([42, -1, 33], variant='sanger')
self.assertIn('-1', str(cm.exception))
self.assertIn('[0, 93]', str(cm.exception))
obs = npt.assert_warns(UserWarning, _encode_phred_to_qual,
[42, 94, 33], variant='sanger')
self.assertEqual(obs, 'K~B')
def test_illumina13_variant(self):
# test entire range of possible ascii chars for illumina1.3
all_illumina13_ascii = ('@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijk'
'lmnopqrstuvwxyz{|}~')
obs = _encode_phred_to_qual(list(range(63)), variant='illumina1.3')
self.assertEqual(obs, all_illumina13_ascii)
with self.assertRaises(ValueError) as cm:
_encode_phred_to_qual([42, -1, 33], variant='illumina1.3')
self.assertIn('-1', str(cm.exception))
self.assertIn('[0, 62]', str(cm.exception))
obs = npt.assert_warns(UserWarning, _encode_phred_to_qual,
[42, 63, 33], variant='illumina1.3')
self.assertEqual(obs, 'j~a')
def test_illumina18_variant(self):
# test entire range of possible ascii chars for illumina1.8
all_illumina18_ascii = ('!"#$%&\'()*+,-./0123456789:;<=>?@ABCDEFGHIJKL'
'MNOPQRSTUVWXYZ[\\]^_')
obs = _encode_phred_to_qual(list(range(63)), variant='illumina1.8')
self.assertEqual(obs, all_illumina18_ascii)
with self.assertRaises(ValueError) as cm:
_encode_phred_to_qual([42, -1, 33], variant='illumina1.8')
self.assertIn('-1', str(cm.exception))
self.assertIn('[0, 62]', str(cm.exception))
obs = npt.assert_warns(UserWarning, _encode_phred_to_qual,
[42, 63, 33], variant='illumina1.8')
self.assertEqual(obs, 'K_B')
def test_custom_phred_offset(self):
ascii_chars = '*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\'
obs = _encode_phred_to_qual(list(range(51)), phred_offset=42)
self.assertEqual(obs, ascii_chars)
with self.assertRaises(ValueError) as cm:
_encode_phred_to_qual([42, -1, 33], phred_offset=42)
self.assertIn('-1', str(cm.exception))
self.assertIn('[0, 84]', str(cm.exception))
obs = npt.assert_warns(UserWarning, _encode_phred_to_qual,
[42, 255, 33], phred_offset=42)
self.assertEqual(obs, 'T~K')
class TestGetNthSequence(unittest.TestCase):
def setUp(self):
def generator():
for i in range(1, 6):
yield 'goldilocks: ' + str(i)
self.gen = generator()
def test_seq_num_too_small(self):
with self.assertRaises(ValueError) as cm:
_get_nth_sequence(self.gen, 0)
self.assertIn('between 1 and', str(cm.exception))
self.assertIn('0', str(cm.exception))
def test_seq_num_too_big(self):
with self.assertRaises(ValueError) as cm:
_get_nth_sequence(self.gen, 6)
self.assertIn('end of file', str(cm.exception))
self.assertIn('6th', str(cm.exception))
def test_seq_num_just_right(self):
value = _get_nth_sequence(self.gen, 3)
self.assertEqual(value, 'goldilocks: 3')
class TestParseFASTALikeHeader(unittest.TestCase):
def test_no_id_or_description(self):
obs = _parse_fasta_like_header('> \t\t \n')
self.assertEqual(obs, ('', ''))
def test_id_only(self):
obs = _parse_fasta_like_header('>suht! \t\t \n')
self.assertEqual(obs, ('suht!', ''))
def test_description_only(self):
obs = _parse_fasta_like_header('> suht! \t\t \n')
self.assertEqual(obs, ('', 'suht!'))
def test_id_and_description(self):
obs = _parse_fasta_like_header('>!thus suht! \t\t \n')
self.assertEqual(obs, ('!thus', 'suht!'))
class TestFormatFASTALikeRecords(unittest.TestCase):
def setUp(self):
def generator():
yield Sequence('ACGT', metadata={'id': '', 'description': ''},
positional_metadata={'quality': range(4)})
yield RNA('GAU', metadata={'id': ' foo \t\t bar ',
'description': ''})
yield DNA('TAG',
metadata={'id': '', 'description': 'foo\n\n bar\n'})
yield Sequence('A',
metadata={'id': 'foo', 'description': 'bar baz'},
positional_metadata={'quality': [42]})
self.gen = generator()
def test_no_replacement(self):
exp = [
('', 'ACGT', range(4)),
(' foo \t\t bar ', 'GAU', None),
(' foo\n\n bar\n', 'TAG', None),
('foo bar baz', 'A', [42])
]
obs = list(_format_fasta_like_records(self.gen, None, None, False))
self.assertEqual(len(obs), len(exp))
for o, e in zip(obs, exp):
npt.assert_equal(o, e)
def test_empty_str_replacement(self):
exp = [
('', 'ACGT', range(4)),
('foobar', 'GAU', None),
(' foo bar', 'TAG', None),
('foo bar baz', 'A', [42])
]
obs = list(_format_fasta_like_records(self.gen, '', '', False))
self.assertEqual(len(obs), len(exp))
for o, e in zip(obs, exp):
npt.assert_equal(o, e)
def test_multi_char_replacement(self):
exp = [
('', 'ACGT', range(4)),
('-.--.-foo-.--.--.--.-bar-.-', 'GAU', None),
(' foo_-__-_ bar_-_', 'TAG', None),
('foo bar baz', 'A', [42])
]
obs = list(_format_fasta_like_records(self.gen, '-.-', '_-_', False))
self.assertEqual(len(obs), len(exp))
for o, e in zip(obs, exp):
npt.assert_equal(o, e)
def test_newline_character_in_id_whitespace_replacement(self):
with self.assertRaisesRegex(ValueError, 'Newline character'):
list(_format_fasta_like_records(self.gen, '-\n--', ' ', False))
def test_newline_character_in_description_newline_replacement(self):
with self.assertRaisesRegex(ValueError, 'Newline character'):
list(_format_fasta_like_records(self.gen, None, 'a\nb', False))
def test_empty_sequence(self):
def blank_seq_gen():
yield from (DNA('A'), Sequence(''), RNA('GG'))
with self.assertRaisesRegex(ValueError, '2nd.*empty'):
list(_format_fasta_like_records(blank_seq_gen(), None, None,
False))
def test_missing_quality_scores(self):
def missing_qual_gen():
yield from (RNA('A', positional_metadata={'quality': [42]}),
Sequence('AG'),
DNA('GG', positional_metadata={'quality': [41, 40]}))
with self.assertRaisesRegex(ValueError,
'2nd sequence.*quality scores'):
list(_format_fasta_like_records(missing_qual_gen(), '-', '-',
True))
if __name__ == '__main__':
unittest.main()
|
