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
|
#!/usr/bin/env python
"""Tests of the Enumeration and Alphabet objects.
Note: individual Alphabets are typically in MolType and are tested there.
"""
from cogent.core.alphabet import Enumeration, get_array_type, \
uint8, uint16, uint32, array, JointEnumeration, CharAlphabet, \
_make_translation_tables, _make_complement_array
from cogent.core.moltype import RNA
from cogent.util.unit_test import TestCase, main
DnaBases = CharAlphabet('TCAG')
RnaBases = CharAlphabet('UCAG')
AminoAcids = CharAlphabet('ACDEFGHIKLMNPQRSTVWY')
__author__ = "Rob Knight, Peter Maxwell and Gavin Huttley"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Peter Maxwell", "Rob Knight", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
class translation_table_tests(TestCase):
"""Tests of top-level translation table functions"""
def test_make_translation_tables(self):
"""_make_translation_tables should translate from chars to indices"""
a = 'ucag'
itoa, atoi = _make_translation_tables(a)
s = 'ggacu'
obs = s.translate(atoi)
self.assertEqual(obs, '\x03\x03\x02\x01\x00')
orig = obs.translate(itoa)
self.assertEqual(orig, s)
def test_make_complement_array(self):
"""_make_complement_array should identify complements correctly"""
complement_array = _make_complement_array(RNA.Alphabet, RNA.Complements)
test = 'UCAG'
test_array = [RNA.Alphabet.index(i) for i in test]
complements = complement_array.take(test_array)
result = ''.join([RNA.Alphabet[i] for i in complements])
self.assertEqual(result, 'AGUC')
class get_array_type_tests(TestCase):
"""Tests of the get_array_type top-level function."""
def test_get_array_type(self):
"""get_array_type should return unsigned type that fits elements."""
self.assertEqual(get_array_type(0), uint8)
self.assertEqual(get_array_type(100), uint8)
self.assertEqual(get_array_type(256), uint8) #boundary case
self.assertEqual(get_array_type(257), uint16) #boundary case
self.assertEqual(get_array_type(10000), uint16)
self.assertEqual(get_array_type(65536), uint16)
self.assertEqual(get_array_type(65537), uint32)
class EnumerationTests(TestCase):
"""Tests of the Enumeration object."""
def test_init(self):
"""Enumeration init should work from any sequence"""
a = Enumeration('abc')
self.assertEqual(a.index('a'), 0)
self.assertEqual(a.index('b'), 1)
self.assertEqual(a.index('c'), 2)
self.assertEqual(a[0], 'a')
self.assertEqual(a[1], 'b')
self.assertEqual(a[2], 'c')
self.assertEqual(a.ArrayType, uint8)
a = Enumeration('bca')
self.assertEqual(a.index('b'), 0)
self.assertEqual(a.index('c'), 1)
self.assertEqual(a.index('a'), 2)
self.assertEqual(a[0], 'b')
self.assertEqual(a[1], 'c')
self.assertEqual(a[2], 'a')
a = Enumeration([1,'2'])
self.assertEqual(a.index(1), 0)
self.assertEqual(a.index('2'), 1)
self.assertRaises(KeyError, a.index, '1')
#check that it works with gaps
a = Enumeration('ab-', '-')
self.assertEqual(a.Gap, '-')
self.assertEqual(a.GapIndex, 2)
a = Enumeration(range(257)) #too big to fit in uint8
self.assertEqual(a.ArrayType, uint16)
def test_index(self):
"""Enumeration index should return first index of item"""
a = Enumeration('bca')
self.assertEqual(a.index('b'), 0)
self.assertEqual(a.index('c'), 1)
self.assertEqual(a.index('a'), 2)
def test_getitem(self):
"""Enumeration[i] should return character at i"""
a = Enumeration('bca')
self.assertEqual(a[0], 'b')
self.assertEqual(a[1], 'c')
self.assertEqual(a[2], 'a')
def test_toIndices(self):
"""Enumeration toIndices should return indices from elements"""
a = Enumeration('bca')
self.assertEqual(a.toIndices(''), [])
self.assertEqual(a.toIndices('ccabac'), [1,1,2,0,2,1])
def test_isValid(self):
"""Enumeration isValid should return True for valid sequence"""
a = Enumeration('bca')
self.assertEqual(a.isValid(''), True)
self.assertEqual(a.isValid('bbb'), True)
self.assertEqual(a.isValid('bbbaac'), True)
self.assertEqual(a.isValid('bbd'), False)
self.assertEqual(a.isValid('d'), False)
self.assertEqual(a.isValid(['a', 'b']), True)
self.assertEqual(a.isValid(['a', None]), False)
def test_fromIndices(self):
"""Enumeration fromIndices should return elements from indices"""
a = Enumeration('bca')
self.assertEqual(a.fromIndices([]), [])
self.assertEqual(a.fromIndices([1,1,2,0,2,1]), list('ccabac'))
def test_pow(self):
"""Enumeration pow should produce JointEnumeration with n copies"""
a = AminoAcids**3
self.assertEqual(a[0], (AminoAcids[0],)*3)
self.assertEqual(a[-1], (AminoAcids[-1],)*3)
self.assertEqual(len(a), len(AminoAcids)**3)
self.assertEqual(a.ArrayType, uint16)
#check that it works with gaps
a = Enumeration('a-b', '-')
b = a**3
self.assertEqual(len(b), 27)
self.assertEqual(b.Gap, ('-','-','-'))
self.assertEqual(b.GapIndex, 13)
self.assertEqual(b.ArrayType, uint8)
#check that array type is set correctly if needed
b = a**6 #too big to fit in char
self.assertEqual(b.ArrayType, uint16)
def test_mul(self):
"""Enumeration mul should produce correct JointEnumeration"""
a = DnaBases * RnaBases
self.assertEqual(len(a), 16)
self.assertEqual(a[0], ('T','U'))
self.assertEqual(a[-1], ('G','G'))
#check that it works with gaps
a = Enumeration('ab-','-')
b = Enumeration('xz','z')
x = a*b
self.assertEqual(x.Gap, ('-','z'))
self.assertEqual(x.GapIndex, 5)
self.assertEqual(len(x), 6)
self.assertEqual(x, (('a','x'),('a','z'),('b','x'),('b','z'),('-','x'),\
('-','z')))
#check that it doesn't work when only one seq has gaps
c = Enumeration('c')
x = a*c
self.assertEqual(x.Gap, None)
def test_counts(self):
"""Enumeration counts should count freqs in array"""
a = DnaBases
f = array([[0,0,1,0,0,3]])
self.assertEqual(a.counts(f), array([4,1,0,1]))
#check that it works with byte array
f = array([[0,0,1,0,0,3]], 'B')
self.assertEqual(a.counts(f), array([4,1,0,1]))
#should ignore out-of-bounds items
g = [0,4]
self.assertEqual(a.counts(g), array([1,0,0,0]))
#make sure it works for long sequences, i.e. no wraparound at 255
h = [0, 3] * 70000
self.assertEqual(a.counts(h), array([70000,0,0,70000]))
h2 = array(h).astype('B')
self.assertEqual(a.counts(h2), array([70000,0,0,70000]))
i = array([0,3] * 75000)
self.assertEqual(a.counts(i), array([75000,0,0,75000]))
#make sure it works for long _binary_ sequences, e.g. the results
#of array comparisons.
a = array([0,1,2,3]*10000)
b = array([0,0,0,0]*10000)
same = (a==b)
class CharAlphabetTests(TestCase):
"""Tests of CharAlphabets."""
def test_init(self):
"""CharAlphabet init should make correct translation tables"""
r = CharAlphabet('UCAG')
i2c, c2i = r._indices_to_chars, r._chars_to_indices
s = array([0,0,1,0,3,2], 'b').tostring()
self.assertEqual(s.translate(i2c), 'UUCUGA')
self.assertEqual('UUCUGA'.translate(c2i), '\000\000\001\000\003\002')
def test_fromString(self):
"""CharAlphabet fromString should return correct array"""
r = CharAlphabet('UCAG')
self.assertEqual(r.fromString('UUCUGA'), array([0,0,1,0,3,2],'B'))
def test_isValid(self):
"""CharAlphabet isValid should return True for valid sequence"""
a = CharAlphabet('bca')
self.assertEqual(a.isValid(''), True)
self.assertEqual(a.isValid('bbb'), True)
self.assertEqual(a.isValid('bbbaac'), True)
self.assertEqual(a.isValid('bbd'), False)
self.assertEqual(a.isValid('d'), False)
self.assertEqual(a.isValid(['a', 'b']), True)
self.assertEqual(a.isValid(['a', None]), False)
def test_fromArray(self):
"""CharAlphabet fromArray should return correct array"""
r = CharAlphabet('UCAG')
self.assertEqual(r.fromArray(array(['UUC','UGA'], 'c')), \
array([[0,0,1],[0,3,2]], 'B'))
def test_toChars(self):
"""CharAlphabet toChars should convert an input array to chars"""
r = CharAlphabet('UCAG')
c = r.toChars(array([[0,0,1],[0,3,2]], 'B'))
self.assertEqual(c, \
array(['UUC','UGA'], 'c'))
def test_toString(self):
"""CharAlphabet toString should convert an input array to string"""
r = CharAlphabet('UCAG')
self.assertEqual(r.toString(array([[0,0,1],[0,3,2]], 'B')), 'UUC\nUGA')
#should work with single seq
self.assertEqual(r.toString(array([[0,0,1,0,3,2]], 'B')), 'UUCUGA')
#should work with single seq
self.assertEqual(r.toString(array([0,0,1,0,3,2], 'B')), 'UUCUGA')
#should work with empty seq
self.assertEqual(r.toString(array([], 'B')), '')
def test_pairs(self):
"""pairs should cache the same object."""
r = CharAlphabet('UCAG')
rp = r.Pairs
self.assertEqual(len(rp), 16)
rp2 = r.Pairs
self.assertSameObj(rp, rp2)
def test_triples(self):
"""triples should cache the same object."""
r = CharAlphabet('UCAG')
rt = r.Triples
self.assertEqual(len(rt), 64)
rt2 = r.Triples
self.assertSameObj(rt, rt2)
class JointEnumerationTests(TestCase):
"""Tests of JointEnumerations."""
def test_init(self):
"""JointEnumeration init should work as expected"""
#should work for alphabet object
a = JointEnumeration([DnaBases, RnaBases])
self.assertEqual(len(a), 16)
self.assertEqual(a.Shape, (4,4))
self.assertEqual(a[0], ('T','U'))
self.assertEqual(a[-1], ('G','G'))
self.assertEqual(a._sub_enum_factors, array([[4],[1]]))
#should work for arbitrary sequences
a = JointEnumeration(['TCAG', 'UCAG'])
self.assertEqual(len(a), 16)
self.assertEqual(a[0], ('T','U'))
self.assertEqual(a[-1], ('G','G'))
self.assertEqual(a._sub_enum_factors, array([[4],[1]]))
#should work for different length sequences
a = JointEnumeration(['TCA', 'UCAG'])
self.assertEqual(a.Shape, (3,4))
self.assertEqual(len(a), 12)
self.assertEqual(a[0], ('T','U'))
self.assertEqual(a[-1], ('A','G'))
self.assertEqual(a._sub_enum_factors, \
array([[4],[1]])) #note: _not_ [3,1]
def test_toIndices(self):
"""JointEnumeration toIndices should convert tuples correctly"""
a = JointEnumeration(['TCAG','UCAG'])
i = a.toIndices([('T','U'),('G','G'),('G','G')])
self.assertEqual(i, [0, 15, 15])
def test_fromIndices(self):
"""JointEnumeration fromIndices should return correct tuples"""
a = JointEnumeration(['TCAG','UCAG'])
i = a.fromIndices([0, 15, 15])
self.assertEqual(i, [('T','U'),('G','G'),('G','G')])
def test_packArrays(self):
"""JointEnumeration packArrays should return correct array."""
a = JointEnumeration(['xyz', 'abcd', 'ef'])
v = [[0,1,2,0],[3,3,1,0], [1,1,0,0]]
result = a.packArrays(v)
self.assertEqual(result, array([7,15,18,0]))
def test_unpackArrays(self):
"""JointEnumeration unpackArrays should return correct arrays."""
a = JointEnumeration(['xyz', 'abcd', 'ef'])
v = [7,15,18,0]
result = a.unpackArrays(v)
self.assertEqual(result, array([[0,1,2,0],[3,3,1,0], [1,1,0,0]]))
if __name__ == '__main__':
main()
|
