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
382
383
384
385
386
387
388
|
#!/usr/bin/env python
# File created on 07 Jul 2012
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
from glob import glob
from shutil import rmtree
from os.path import exists, join
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import create_dir, remove_files
from biom.parse import parse_biom_table
from qiime.test import initiate_timeout, disable_timeout
from qiime.util import get_qiime_temp_dir, get_tmp_filename
from qiime.parse import parse_otu_map
from qiime.parallel.map_reads_to_reference import \
(ParallelDatabaseMapperUsearch, ParallelDatabaseMapperBlat,
ParallelDatabaseMapperBwaShort)
class ParallelDatabaseMapperTests(TestCase):
def setUp(self):
""" """
self.files_to_remove = []
self.dirs_to_remove = []
tmp_dir = get_qiime_temp_dir()
self.test_out = get_tmp_filename(tmp_dir=tmp_dir,
prefix='qiime_parallel_tests_',
suffix='',
result_constructor=str)
self.dirs_to_remove.append(self.test_out)
create_dir(self.test_out)
self.refseqs1_fp = get_tmp_filename(tmp_dir=self.test_out,
prefix='qiime_refseqs',
suffix='.fasta')
refseqs1_f = open(self.refseqs1_fp,'w')
refseqs1_f.write(refseqs1)
refseqs1_f.close()
self.files_to_remove.append(self.refseqs1_fp)
self.refseqs2_fp = get_tmp_filename(tmp_dir=self.test_out,
prefix='qiime_refseqs',
suffix='.fasta')
refseqs2_f = open(self.refseqs2_fp,'w')
refseqs2_f.write(refseqs2)
refseqs2_f.close()
self.files_to_remove.append(self.refseqs2_fp)
self.inseqs1_fp = get_tmp_filename(tmp_dir=self.test_out,
prefix='qiime_inseqs',
suffix='.fasta')
inseqs1_f = open(self.inseqs1_fp,'w')
inseqs1_f.write(inseqs1)
inseqs1_f.close()
self.files_to_remove.append(self.inseqs1_fp)
self.inseqs2_fp = get_tmp_filename(tmp_dir=self.test_out,
prefix='qiime_inseqs',
suffix='.fasta')
inseqs2_f = open(self.inseqs2_fp,'w')
inseqs2_f.write(inseqs2)
inseqs2_f.close()
self.files_to_remove.append(self.inseqs2_fp)
initiate_timeout(60)
def tearDown(self):
""" """
disable_timeout()
remove_files(self.files_to_remove)
# remove directories last, so we don't get errors
# trying to remove files which may be in the directories
for d in self.dirs_to_remove:
if exists(d):
rmtree(d)
class ParallelDatabaseMapperUsearchTests(ParallelDatabaseMapperTests):
def test_parallel_database_mapper_usearch(self):
""" parallel_database_mapper_usearch functions as expected """
params = {'refseqs_fp':self.refseqs1_fp,
'min_percent_id':0.97,
'evalue':1e-10,
'max_accepts':1,
'max_rejects':32,
'queryalnfract':0.35,
'targetalnfract':0.0,
'observation_metadata_fp':None
}
app = ParallelDatabaseMapperUsearch()
r = app(self.inseqs1_fp,
self.test_out,
params,
job_prefix='PTEST',
poll_directly=True,
suppress_submit_jobs=False)
observation_map_fp = glob(join(self.test_out,'observation_map.txt'))[0]
omap = parse_otu_map(open(observation_map_fp,'U'))
self.assertEqual(len(omap[0]),3)
self.assertEqualItems(omap[1],['eco:b0015', 'eco:b0122','eco:b0015:duplicate'])
self.assertEqualItems(omap[2],['eco:b0015-pr', 'eco:b0122-pr'])
class ParallelDatabaseMapperBlatTests(ParallelDatabaseMapperTests):
def test_parallel_database_mapper_blat(self):
""" parallel_database_mapper_blat functions as expected """
params = {'refseqs_fp':self.refseqs1_fp,
'min_percent_id':0.97,
'evalue':1e-10,
'max_accepts':1,
'max_rejects':32,
'queryalnfract':0.35,
'targetalnfract':0.0,
'observation_metadata_fp':None
}
app = ParallelDatabaseMapperBlat()
r = app(self.inseqs1_fp,
self.test_out,
params,
job_prefix='PTEST',
poll_directly=True,
suppress_submit_jobs=False)
observation_map_fp = glob(join(self.test_out,'observation_map.txt'))[0]
omap = parse_otu_map(open(observation_map_fp,'U'))
self.assertEqual(len(omap[0]),3)
self.assertEqualItems(omap[1],['eco:b0015', 'eco:b0122','eco:b0015:duplicate'])
self.assertEqualItems(omap[2],['eco:b0015-pr', 'eco:b0122-pr'])
class ParallelDatabaseMapperBwaShortTests(ParallelDatabaseMapperTests):
def test_bwa_short_database_mapper(self):
"""bwa_short_database_mapper functions as expected """
params = {'refseqs_fp':self.refseqs2_fp,
'max_diff':None,
'observation_metadata_fp':None}
app = ParallelDatabaseMapperBwaShort()
r = app(self.inseqs2_fp,
self.test_out,
params,
poll_directly=True,
suppress_submit_jobs=False)
observation_map_fp = join(self.test_out,'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out,'observation_table.biom')
table = parse_biom_table(open(observation_table_fp,'U'))
self.assertEqualItems(table.SampleIds,['s2','s1'])
self.assertEqualItems(table.ObservationIds,['r1','r2','r3','r4','r5'])
self.assertEqual(table.sum(),6)
def test_bwa_short_database_mapper_alt_params(self):
"""bwa_short_database_mapper functions as expected """
params = {'refseqs_fp':self.refseqs2_fp,
'max_diff':1,
'observation_metadata_fp':None}
app = ParallelDatabaseMapperBwaShort()
r = app(self.inseqs2_fp,
self.test_out,
params,
poll_directly=True,
suppress_submit_jobs=False)
observation_map_fp = join(self.test_out,'observation_map.txt')
self.assertTrue(exists(observation_map_fp))
observation_table_fp = join(self.test_out,'observation_table.biom')
table = parse_biom_table(open(observation_table_fp,'U'))
self.assertEqualItems(table.SampleIds,['s2','s1'])
self.assertEqualItems(table.ObservationIds,['r2','r3','r4','r5'])
self.assertEqual(table.sum(),5)
refseqs1 = """>eco:b0001-pr
MKRISTTITTTITITTGNGAG
>eco:b0015-pr dnaJ
MAKQDYYEILGVSKTAEEREIRKAYKRLAMKYHPDRNQGDKEAEAKFKEIKEAYEVLTDS
QKRAAYDQYGHAAFEQGGMGGGGFGGGADFSDIFGDVFGDIFGGGRGRQRAARGADLRYN
MELTLEEAVRGVTKEIRIPTLEECDVCHGSGAKPGTQPQTCPTCHGSGQVQMRQGFFAVQ
QTCPHCQGRGTLIKDPCNKCHGHGRVERSKTLSVKIPAGVDTGDRIRLAGEGEAGEHGAP
AGDLYVQVQVKQHPIFEREGNNLYCEVPINFAMAALGGEIEVPTLDGRVKLKVPGETQTG
KLFRMRGKGVKSVRGGAQGDLLCRVVVETPVGLNERQKQLLQELQESFGGPTGEHNSPRS
KSFFDGVKKFFDDLTR
>eco:b0122-pr
MKTFFRTVLFGSLMAVCANSYALSESEAEDMADLTAVFVFLKNDCGYQNLPNGQIRRALV
FFAQQNQWDLSNYDTFDMKALGEDSYRDLSGIGIPVAKKCKALARDSLSLLAYVK
"""
refseqs2 = """>r1
atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcg
ggctga
>r2 some comments...
atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgagaa
>r3
atgaagacgtttttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaataa
>r4
atgaagaaaattttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaatcc
>r5 some comments...
aatgactaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa
"""
inseqs1 = """>eco:b0001 thrL; thr operon leader peptide; K08278 thr operon leader peptide (N)
atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcg
ggctga
>eco:b0015 dnaJ; chaperone Hsp40, co-chaperone with DnaK; K03686 molecular chaperone DnaJ (N)
atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa
>eco:b0122
atgaagacgtttttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaataa
>eco:b0015:duplicate
atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa
"""
inseqs2 = """>s1_1
atgttacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcg
ggctga
>s2_2 some comments...
atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgagaa
>s1_3
atgaagacgtttttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaataa
>s1_4
atgaagaaaattttcagaacagtgttattcggcagcctgatggccgtctgcgcaaacagt
tacgcgctcagcgagtctgaagccgaagatatggccgatttaacggcagtttttgtcttt
ctgaagaacgattgtggttaccagaacttacctaacgggcaaattcgtcgcgcactggtc
tttttcgctcagcaaaaccagtgggacctcagtaattacgacaccttcgacatgaaagcc
ctcggtgaagacagctaccgcgatctcagcggcattggcattcccgtcgctaaaaaatgc
aaagccctggcccgcgattccttaagcctgcttgcctacgtcaaatcc
>s1_5
atggctaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa
>s1_6 some comments...
aatgactaagcaagattattacgagattttaggcgtttccaaaacagcggaagagcgtgaa
atcagaaaggcctacaaacgcctggccatgaaataccacccggaccgtaaccagggtgac
aaagaggccgaggcgaaatttaaagagatcaaggaagcttatgaagttctgaccgactcg
caaaaacgtgcggcatacgatcagtatggtcatgctgcgtttgagcaaggtggcatgggc
ggcggcggttttggcggcggcgcagacttcagcgatatttttggtgacgttttcggcgat
atttttggcggcggacgtggtcgtcaacgtgcggcgcgcggtgctgatttacgctataac
atggagctcaccctcgaagaagctgtacgtggcgtgaccaaagagatccgcattccgact
ctggaagagtgtgacgtttgccacggtagcggtgcaaaaccaggtacacagccgcagact
tgtccgacctgtcatggttctggtcaggtgcagatgcgccagggattcttcgctgtacag
cagacctgtccacactgtcagggccgcggtacgctgatcaaagatccgtgcaacaaatgt
catggtcatggtcgtgttgagcgcagcaaaacgctgtccgttaaaatcccggcaggggtg
gacactggagaccgcatccgtcttgcgggcgaaggtgaagcgggcgagcatggcgcaccg
gcaggcgatctgtacgttcaggttcaggttaaacagcacccgattttcgagcgtgaaggc
aacaacctgtattgcgaagtcccgatcaacttcgctatggcggcgctgggtggcgaaatc
gaagtaccgacccttgatggtcgcgtcaaactgaaagtgcctggcgaaacccagaccggt
aagctattccgtatgcgcggtaaaggcgtcaagtctgtccgcggtggcgcacagggtgat
ttgctgtgccgcgttgtcgtcgaaacaccggtaggcctgaacgaaaggcagaaacagctg
ctgcaagagctgcaagaaagcttcggtggcccaaccggcgagcacaacagcccgcgctca
aagagcttctttgatggtgtgaagaagttttttgacgacctgacccgctaa
"""
if __name__ == "__main__":
main()
|
