/
test_deblurring.py
367 lines (334 loc) · 17.6 KB
/
test_deblurring.py
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
# -----------------------------------------------------------------------------
# Copyright (c) 2015, The Deblur Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# -----------------------------------------------------------------------------
from unittest import TestCase, main
from io import StringIO
from os.path import join, dirname, abspath
import skbio
import numpy as np
from deblur.sequence import Sequence
from deblur.workflow import sequence_generator
from deblur.deblurring import get_sequences, deblur, get_default_error_profile
class DeblurringTests(TestCase):
def setUp(self):
self.seqs = [("151_9240;size=170;", "---tagggcaagactccatggt-----"),
("151_6640;size=1068;", "---cggaggcgagatgcgtggt-----"),
("151_64278;size=200;", "---tactagcaagattcctggt-----"),
("151_4447;size=1812;", "---aggatgcgagatgcgtggt-----"),
("151_14716;size=390;", "---gagtgcgagatgcgtggtg-----"),
("151_3288;size=1337;", "---ggatgcgagatgcgtggtg-----"),
("151_41690;size=157;", "---agg-gcgagattcctagtgg----"),
("151_5155;size=998;", "---gaggatgcgagatgcgtgg-----"),
("151_527;size=964;", "---acggaggatgatgcgcggt-----"),
("151_5777;size=305;", "---ggagtgcaagattccaggt-----")]
self.test_data_dir = join(dirname(abspath(__file__)), 'data')
def test_get_default_error_profile(self):
goodprofile = [1, 0.06, 0.02, 0.02, 0.01,
0.005, 0.005, 0.005, 0.001, 0.001,
0.001, 0.0005]
self.assertEqual(goodprofile, get_default_error_profile())
def test_get_sequences_error_real_length(self):
seqs = [("151_9240;size=170;", "----tagggcaagactccatg-----"),
("151_6640;size=1068;", "--acggaggcga-atgcgtggt----"),
("151_64278;size=200;", "---tactagcaagattcctgg-----")]
with self.assertRaises(ValueError):
get_sequences(seqs)
def test_get_sequences_error_length(self):
seqs = [("151_9240;size=170;", "----tagggcaagactccatg----"),
("151_6640;size=1068;", "--acggaggcgagatgcgtggt----"),
("151_64278;size=200;", "---tactagcaagattcctgg-----")]
with self.assertRaises(ValueError):
get_sequences(seqs)
def test_get_sequences_empty_file(self):
gen = skbio.read(join(self.test_data_dir, 'seqs_empty.fasta'),
format='fasta')
self.assertEqual(get_sequences(gen), None)
def test_get_sequences_error_empty(self):
self.assertIsNone(get_sequences([]))
def test_deblur_noseqs(self):
"""If no sequences supplied, need to return None
"""
res = deblur([])
self.assertEqual(res, None)
def test_get_sequences(self):
exp_seqs = [
Sequence("151_4447;size=1812;", "---aggatgcgagatgcgtggt-----"),
Sequence("151_3288;size=1337;", "---ggatgcgagatgcgtggtg-----"),
Sequence("151_6640;size=1068;", "---cggaggcgagatgcgtggt-----"),
Sequence("151_5155;size=998;", "---gaggatgcgagatgcgtgg-----"),
Sequence("151_527;size=964;", "---acggaggatgatgcgcggt-----"),
Sequence("151_14716;size=390;", "---gagtgcgagatgcgtggtg-----"),
Sequence("151_5777;size=305;", "---ggagtgcaagattccaggt-----"),
Sequence("151_64278;size=200;", "---tactagcaagattcctggt-----"),
Sequence("151_9240;size=170;", "---tagggcaagactccatggt-----"),
Sequence("151_41690;size=157;", "---agg-gcgagattcctagtgg----")]
obs_seqs = get_sequences(self.seqs)
self.assertEqual(obs_seqs, exp_seqs)
def test_deblur_toy_example(self):
seqs_f = StringIO(TEST_SEQS_1)
obs = deblur(sequence_generator(seqs_f))
exp = [
Sequence("E.Coli;size=1000;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag")]
self.assertEqual(obs, exp)
def test_deblur(self):
seqs_f = StringIO(TEST_SEQS_2)
obs = deblur(sequence_generator(seqs_f))
exp = [
Sequence("E.Coli-999;size=720;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag")]
self.assertEqual(obs, exp)
def test_deblur_indel(self):
"""Test if also removes indel sequences
"""
seqs_f = StringIO(TEST_SEQS_2)
# add the MSA for the indel
seqs = sequence_generator(seqs_f)
newseqs = []
for chead, cseq in seqs:
tseq = cseq[:10] + '-' + cseq[10:]
newseqs.append((chead, tseq))
# now add a sequence with an A insertion
tseq = cseq[:10] + 'A' + cseq[10:-1]+'-'
newseqs.append((chead, tseq))
obs = deblur(newseqs)
# remove the '-' (same as in launch_workflow)
for s in obs:
s.sequence = s.sequence.replace('-', '')
# the expected output
exp = [
Sequence("E.Coli-999;size=720;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag")]
# make sure we get 1 sequence as output
self.assertEqual(len(obs), 1)
# and that it is the correct sequence
self.assertEqual(obs[0].sequence, exp[0].sequence)
def test_deblur_with_non_default_error_profile(self):
error_dist = [1, 0.05, 0.000005, 0.000005, 0.000005, 0.000005,
0.0000025, 0.0000025, 0.0000025, 0.0000025, 0.0000025,
0.0000005, 0.0000005, 0.0000005, 0.0000005]
seqs_f = StringIO(TEST_SEQS_2)
obs = deblur(sequence_generator(seqs_f), error_dist=error_dist)
exp = [
Sequence("E.Coli-999;size=720;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag")]
self.assertEqual(obs, exp)
error_dist = np.array(
[1, 0.06, 0.02, 0.02, 0.01,
0.005, 0.005, 0.005, 0.001,
0.001, 0.001, 0.0005])
seqs_f = StringIO(TEST_SEQS_2)
obs = deblur(sequence_generator(seqs_f), error_dist=error_dist)
exp = [
Sequence("E.Coli-999;size=720;",
"tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggt"
"ttgttaagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactg"
"gcaagcttgagtctcgtagaggggggcagaattccag")]
self.assertEqual(obs, exp)
TEST_SEQS_1 = """>E.Coli;size=1000;
tacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggtttgt
taagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactggcaagctt
gagtctcgtagaggggggcagaattccag
>Error;size=3;
aacggagggtgcaagcgttaatcggaattactgggcgtaaagcgcacgcaggcggtttgt
taagtcagatgtgaaatccccgggctcaacctgggaactgcatctgatactggcaagctt
gagtctcgtagaggggggcagaattccag
"""
TEST_SEQS_2 = """>E.Coli-999;size=720;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-781;size=5;
TGCGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-987;size=4;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGGCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-861;size=3;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCATGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-791;size=3;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACACAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-832;size=3;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGATTTCCAG
>E.Coli-476;size=3;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAAGCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-633;size=3;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CTGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-894;size=3;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCAAG
>E.Coli-702;size=3;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAAATCCAG
>E.Coli-986;size=3;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGACGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-991;size=3;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGGTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-975;size=3;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGTCAGAATTCCAG
>E.Coli-670;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTCGAGGGGGGCAGAATTCCAG
>E.Coli-709;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGCGGCAGAATTCCAG
>E.Coli-640;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCCCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-831;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAC
>E.Coli-663;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTATCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-645;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCCTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-799;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTTCAG
>E.Coli-807;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGATTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-795;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCGTCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-785;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGAGGGCAGAATTCCAG
>E.Coli-743;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGGATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-737;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATTTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-749;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTGCAG
>E.Coli-818;size=2;
TCCGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-636;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGAAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-235;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCACAATTCCAG
>E.Coli-228;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGATTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-311;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTTGAGGGGGGCAGAATTCCAG
>E.Coli-393;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATATGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-336;size=2;
TACGGAGGGTGCAAGAGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-190;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTGTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-66;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGCCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-198;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAAGGGGGCAGAATTCCAG
>E.Coli-225;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCTAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-216;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGGAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-555;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCGGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-538;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGTCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-561;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CAGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-615;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAAACC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-604;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGAGGGGCAGAATTCCAG
>E.Coli-498;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
TCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-455;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGCCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-507;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTACATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-519;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGAAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-511;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCTG
>E.Coli-983;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGTGGGGGGCAGAATTCCAG
>E.Coli-968;size=2;
TACGGAGGGTGGAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-997;size=2;
TACGGAGGGTGCAAGCCTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-1000;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCTCGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-883;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCACCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-911;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGGACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-963;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACCGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-941;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATGCTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-932;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGGAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-915;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCGACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-917;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACAGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
>E.Coli-838;size=2;
TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGACAGAATTCCAG
>E.Coli-851;size=2;
TACGGAGGGTGCATGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCC
CCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGCAGAATTCCAG
"""
if __name__ == '__main__':
main()