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
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
|
# Copyright 2012 by Andrew Sczesnak. All rights reserved.
# Revisions Copyright 2017 by Blaise Li. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit tests for Bio.AlignIO.MafIO.MafIndex()."""
try:
import sqlite3
except ImportError:
# skip most tests if sqlite is not available
sqlite3 = None
import os
import unittest
import tempfile
import shutil
from Bio.AlignIO.MafIO import MafIndex
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from seq_tests_common import compare_record
class StaticMethodTest(unittest.TestCase):
"""Test static UCSC binning-related functions."""
def test_region2bin(self):
data = [
(25079603, 25079787, {0, 1, 11, 96, 776}),
(25128173, 25128248, {0, 1, 11, 96, 776}),
(50312474, 50312703, {0, 1, 968, 14, 120}),
(41905591, 41906101, {0, 1, 904, 13, 112}),
(16670899, 16673060, {0, 1, 10, 712, 88}),
(75495356, 75495494, {0, 1, 2, 1160, 144, 17}),
(92259501, 92261053, {0, 1, 2, 1288, 160, 19}),
(83834063, 83838132, {0, 1, 2, 1224, 18, 152}),
(7309597, 7310411, {0, 1, 640, 79, 9}),
(6190410, 6190999, {0, 1, 632, 78, 9}),
]
for x, y, z in data:
self.assertEqual(MafIndex._region2bin(x, y), z)
for x, y, z in data:
self.assertRaises(TypeError, MafIndex._region2bin, str(x), str(y))
def test_ucscbin(self):
data = [
(25079603, 25079787, 776),
(25128173, 25128248, 776),
(50312474, 50312703, 968),
(41905591, 41906101, 904),
(16670899, 16673060, 712),
(75495356, 75495494, 1160),
(92259501, 92261053, 1288),
(83834063, 83838132, 1224),
(7309597, 7310411, 640),
(6190410, 6190999, 632),
]
for x, y, z in data:
self.assertEqual(MafIndex._ucscbin(x, y), z)
for x, y, z in data:
self.assertRaises(TypeError, MafIndex._ucscbin, str(x), str(y))
if sqlite3:
class PreBuiltIndexTest(unittest.TestCase):
"""Test loading of prebuilt indices."""
def test_old(self):
idx = MafIndex(
"MAF/ucsc_mm9_chr10.mafindex", "MAF/ucsc_mm9_chr10.maf", "mm9.chr10"
)
self.assertEqual(len(idx), 48)
def test_old_wrong_target_seqname(self):
self.assertRaises(
ValueError,
MafIndex,
"MAF/ucsc_mm9_chr10.mafindex",
"MAF/ucsc_mm9_chr10.maf",
"mm9.chr11",
)
def test_old_wrong_filename(self):
self.assertRaises(
ValueError,
MafIndex,
"MAF/ucsc_mm9_chr10.mafindex",
"MAF/humor.maf",
"mm9.chr10",
)
def test_old_file_not_found(self):
self.assertRaises(
FileNotFoundError,
MafIndex,
"MAF/ucsc_mm9_chr11.mafindex",
"MAF/ucsc_mm9_chr11.maf",
"mm9.chr11",
)
def test_old_wrong_version(self):
self.assertRaises(
ValueError,
MafIndex,
"MAF/wrong_version.idx",
"MAF/ucsc_mm9_chr10.maf",
"mm9.chr10",
)
def test_old_unfinished_index(self):
self.assertRaises(
ValueError,
MafIndex,
"MAF/unfinished.idx",
"MAF/ucsc_mm9_chr10.maf",
"mm9.chr10",
)
def test_old_corrupt_index(self):
self.assertRaises(
ValueError,
MafIndex,
"MAF/corrupt.idx",
"MAF/ucsc_mm9_chr10.maf",
"mm9.chr10",
)
def test_old_invalid_sqlite(self):
self.assertRaises(
ValueError,
MafIndex,
"MAF/invalid.idx",
"MAF/ucsc_mm9_chr10.maf",
"mm9.chr10",
)
class NewIndexTest(unittest.TestCase):
"""Test creation of new indices."""
def setUp(self):
self.tmpdir = tempfile.mkdtemp()
self.tmpfile = self.tmpdir + "/database.sqlite3"
def tearDown(self):
if os.path.isdir(self.tmpdir):
shutil.rmtree(self.tmpdir)
def test_good_small(self):
idx = MafIndex(self.tmpfile, "MAF/ucsc_mm9_chr10.maf", "mm9.chr10")
self.assertEqual(len(idx), 48)
def test_good_big(self):
idx = MafIndex(self.tmpfile, "MAF/ucsc_mm9_chr10_big.maf", "mm9.chr10")
self.assertEqual(len(idx), 983)
def test_bundle_without_target(self):
self.assertRaises(
ValueError,
MafIndex,
self.tmpfile,
"MAF/bundle_without_target.maf",
"mm9.chr10",
)
def test_length_coords_mismatch(self):
self.assertRaises(
ValueError,
MafIndex,
self.tmpfile,
"MAF/length_coords_mismatch.maf",
"mm9.chr10",
)
class TestGetRecord(unittest.TestCase):
"""Make sure we can seek and fetch records properly."""
def setUp(self):
self.idx = MafIndex(
"MAF/ucsc_mm9_chr10.mafindex", "MAF/ucsc_mm9_chr10.maf", "mm9.chr10"
)
self.assertEqual(len(self.idx), 48)
def test_records_begin(self):
recs = {}
recs[0] = SeqRecord(
Seq(
"TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAA"
"CACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTA"
"AAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCAT"
"AGAAGATGACATAATGTATTTTCCTTTTGGTT"
),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={
"start": 3009319,
"srcSize": 129993255,
"strand": 1,
"size": 162,
},
)
recs[1] = SeqRecord(
Seq(
"TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGG"
"TTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCA"
"GAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCAT"
"GGAAACTGATGTCAAATACTTTCCCTTTGGTT"
),
id="oryCun1.scaffold_133159",
name="oryCun1.scaffold_133159",
description="",
annotations={
"start": 11087,
"srcSize": 13221,
"strand": 1,
"size": 164,
},
)
fetched_recs = self.idx._get_record(34)
for i in range(2):
self.assertTrue(compare_record(recs[i], fetched_recs[i]))
def test_records_end(self):
recs = {}
recs[0] = SeqRecord(
Seq("TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt"),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={
"start": 3021494,
"srcSize": 129993255,
"strand": 1,
"size": 42,
},
)
recs[1] = SeqRecord(
Seq("TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="ponAbe2.chr6",
name="ponAbe2.chr6",
description="",
annotations={
"start": 16173516,
"srcSize": 174210431,
"strand": -1,
"size": 46,
},
)
recs[2] = SeqRecord(
Seq("TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="panTro2.chr6",
name="panTro2.chr6",
description="",
annotations={
"start": 16393864,
"srcSize": 173908612,
"strand": -1,
"size": 46,
},
)
recs[3] = SeqRecord(
Seq("TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="hg18.chr6",
name="hg18.chr6",
description="",
annotations={
"start": 15875298,
"srcSize": 170899992,
"strand": -1,
"size": 46,
},
)
recs[4] = SeqRecord(
Seq("TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT"),
id="canFam2.chr1",
name="canFam2.chr1",
description="",
annotations={
"start": 78072287,
"srcSize": 125616256,
"strand": -1,
"size": 46,
},
)
recs[5] = SeqRecord(
Seq("TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----"),
id="ornAna1.chr2",
name="ornAna1.chr2",
description="",
annotations={
"start": 14757144,
"srcSize": 54797317,
"strand": -1,
"size": 36,
},
)
fetched_recs = self.idx._get_record(99228)
for i in range(6):
self.assertTrue(compare_record(recs[i], fetched_recs[i]))
class TestSearchGoodMAF(unittest.TestCase):
"""Test index searching on a properly-formatted MAF."""
def setUp(self):
self.idx = MafIndex(
"MAF/ucsc_mm9_chr10.mafindex", "MAF/ucsc_mm9_chr10.maf", "mm9.chr10"
)
self.assertEqual(len(self.idx), 48)
def test_invalid_type_1(self):
search = self.idx.search((500, 1000), ("string", 1500))
self.assertRaises(TypeError, next, search)
def test_invalid_type_2(self):
search = self.idx.search((500, 1000), (750, 1500.25))
self.assertRaises(TypeError, next, search)
def test_invalid_exon_count(self):
search = self.idx.search((0, 1000, 2000), (500, 1500))
self.assertRaises(ValueError, next, search)
def test_invalid_exon_schema(self):
search = self.idx.search((0, 1000, 2000), (250, 500, 2500))
self.assertRaises(ValueError, next, search)
def test_correct_retrieval_1(self):
"""Correct retrieval of Cnksr3 in mouse."""
search = self.idx.search((3014742, 3018161), (3015028, 3018644))
results = list(search)
self.assertEqual(len(results), 4 + 4)
self.assertEqual({len(x) for x in results}, {4, 1, 9, 10, 4, 3, 5, 1})
# Code formatting note:
# Expected start coordinates are grouped by alignment blocks
# Turn black code style off
# fmt: off
self.assertEqual(
{x.annotations["start"] for y in results for x in y},
{
3014742, 6283, 184202, 1257,
3014778,
3014795, 184257, 6365, 15871286, 16389854, 16169492, 171521, 7816, 1309,
3014842, 1371, 7842, 171548, 16169512, 16389874, 15871306, 6404, 184317, 14750994,
3018161, 16390178, 15871611, 16169818,
3018230, 15871676, 16390243,
3018359, 16390338, 15871771, 184712, 16169976, 3018482
}
)
# Turn black code style on
# fmt: on
def test_correct_retrieval_2(self):
search = self.idx.search((3009319, 3021421), (3012566, 3021536))
results = list(search)
self.assertEqual(len(results), 6)
self.assertEqual({len(x) for x in results}, {2, 4, 5, 14, 7, 6})
# Code formatting note:
# Expected start coordinates are grouped by alignment blocks
# Turn black code style off
# fmt: off
self.assertEqual(
{x.annotations["start"] for y in results for x in y},
{
3009319, 11087,
3012076, 16160203, 16379004, 15860456,
3012441, 15860899, 16379447, 16160646, 180525,
3021421, 9910, 996, 16173434, 16393782, 15875216, 11047, 175213, 3552, 677, 78072203, 3590, 95587, 14757054,
3021465, 9957, 16173483, 16393831, 15875265, 78072243, 14757099,
3021494, 16173516, 16393864, 15875298, 78072287, 14757144
}
)
# Turn black code style on
# fmt: on
def test_correct_retrieval_3(self):
"""Following issue 1083.
https://github.com/biopython/biopython/issues/1083
"""
search = self.idx.search(
(3012076, 3012076 + 300), (3012076 + 100, 3012076 + 400)
)
results = list(search)
self.assertEqual(len(results), 2)
self.assertEqual({len(x) for x in results}, {4, 5})
# Code formatting note:
# Expected start coordinates are grouped by alignment blocks
# Turn black code style off
# fmt: off
self.assertEqual(
{x.annotations["start"] for y in results for x in y},
{
3012076, 16160203, 16379004, 15860456,
3012441, 15860899, 16379447, 16160646, 180525
}
)
# Turn black code style on
# fmt: on
def test_correct_block_boundary(self):
"""Following issues 504 and 1086.
https://github.com/biopython/biopython/pull/504
https://github.com/biopython/biopython/pull/1086#issuecomment-285080702
We test what happens at the boundary between these two MAF blocks:
a score=19159.000000
s mm9.chr10 3014644 45 + 129993255 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG
s hg18.chr6 15870786 46 - 170899992 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
i hg18.chr6 I 9085 C 0
s panTro2.chr6 16389355 46 - 173908612 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
q panTro2.chr6 99999999999999999999999-9999999999999999999-9999
i panTro2.chr6 I 9106 C 0
s calJac1.Contig6394 6182 46 + 133105 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT
i calJac1.Contig6394 N 0 C 0
s loxAfr1.scaffold_75566 1167 34 - 10574 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC
q loxAfr1.scaffold_75566 ------------99999699899-9999999999999869998-9997
i loxAfr1.scaffold_75566 N 0 C 0
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
# Segments ending at the end of the first block
search = self.idx.search([3014687], [3014689])
self.assertEqual(len(list(search)), 1)
search = self.idx.search([3014688], [3014689])
self.assertEqual(len(list(search)), 1)
# Segments starting at the beginning of the second block
search = self.idx.search([3014689], [3014690])
self.assertEqual(len(list(search)), 1)
search = self.idx.search([3014689], [3014691])
self.assertEqual(len(list(search)), 1)
# Segments overlapping the 2 blocks
search = self.idx.search([3014688], [3014690])
self.assertEqual(len(list(search)), 2)
search = self.idx.search([3014687], [3014690])
self.assertEqual(len(list(search)), 2)
search = self.idx.search([3014687], [3014691])
self.assertEqual(len(list(search)), 2)
def test_correct_block_length(self):
"""Following issues 504 and 1086.
https://github.com/biopython/biopython/pull/504
https://github.com/biopython/biopython/pull/1086#issuecomment-285080702
We get the alignement corresponding to the following whole MAF block
and check that the lengths of its sequences are correct:
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
ali = self.idx.get_spliced([3014689], [3014689 + 53])
seq_dict = {seqrec.id: seqrec.seq for seqrec in ali}
correct_lengths = {
"mm9.chr10": 53,
"hg18.chr6": 53,
"panTro2.chr6": 53,
"calJac1.Contig6394": 53,
"otoGar1.scaffold_334.1-359464": 52,
"loxAfr1.scaffold_75566": 54,
}
for seq_id, length in correct_lengths.items():
self.assertEqual(len(seq_dict[seq_id].ungap("-")), length)
def test_correct_spliced_sequences_1(self):
"""Checking that spliced sequences are correct.
We get the alignement corresponding to the following whole MAF block
and check that the sequences are correct:
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
ali = self.idx.get_spliced([3014689], [3014689 + 53])
seq_dict = {seqrec.id: seqrec.seq for seqrec in ali}
correct_sequences = {
"mm9.chr10": "GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCTTTGGAAAGAGTTG",
"hg18.chr6": "GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"panTro2.chr6": "GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"calJac1.Contig6394": "GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTTTGGGAAACAGTGG",
"otoGar1.scaffold_334.1-359464": "GGAAGCATAAACTTTTAATCTATGAAATATCAAATCACTTGGGCAATAGCTG",
"loxAfr1.scaffold_75566": "GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG",
}
for seq_id, sequence in correct_sequences.items():
self.assertEqual(seq_dict[seq_id].ungap("-"), sequence)
def test_correct_spliced_sequences_2(self):
"""Checking that spliced sequences are correct.
We get spliced alignements from following MAF blocks
and check that the sequences are correct:
a score=19159.000000
s mm9.chr10 3014644 45 + 129993255 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG
s hg18.chr6 15870786 46 - 170899992 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
i hg18.chr6 I 9085 C 0
s panTro2.chr6 16389355 46 - 173908612 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
q panTro2.chr6 99999999999999999999999-9999999999999999999-9999
i panTro2.chr6 I 9106 C 0
s calJac1.Contig6394 6182 46 + 133105 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT
i calJac1.Contig6394 N 0 C 0
s loxAfr1.scaffold_75566 1167 34 - 10574 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC
q loxAfr1.scaffold_75566 ------------99999699899-9999999999999869998-9997
i loxAfr1.scaffold_75566 N 0 C 0
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
ali = self.idx.get_spliced([3014644, 3014689], [3014644 + 45, 3014689 + 53])
seq_dict = {seqrec.id: seqrec.seq for seqrec in ali}
correct_sequences = {
"mm9.chr10": "CCTGTACCCTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTGGGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCTTTGGAAAGAGTTG",
"hg18.chr6": "CCTATACCTTTCTTTTATGAGAATTTTGTTTTAATCCTAAACTTTTGGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"panTro2.chr6": "CCTATACCTTTCTTTTATGAGAATTTTGTTTTAATCCTAAACTTTTGGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"calJac1.Contig6394": "CCTATACCTTTCTTTCATGAGAATTTTGTTTGAATCCTAAACTTTTGGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTTTGGGAAACAGTGG",
"otoGar1.scaffold_334.1-359464": "GGAAGCATAAACTTTTAATCTATGAAATATCAAATCACTTGGGCAATAGCTG",
"loxAfr1.scaffold_75566": "TTTGGTTAGAATTATGCTTTAATTCAAAACTTCCGGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG",
}
for seq_id, sequence in correct_sequences.items():
self.assertEqual(seq_dict[seq_id].ungap("-"), sequence)
class TestSearchBadMAF(unittest.TestCase):
"""Test index searching on an incorrectly-formatted MAF."""
def setUp(self):
self.idx = MafIndex(
"MAF/ucsc_mm9_chr10_bad.mafindex",
"MAF/ucsc_mm9_chr10_bad.maf",
"mm9.chr10",
)
self.assertEqual(len(self.idx), 48)
def test_incorrect_bundle_coords(self):
search = self.idx.search((3013219,), (3013319,))
self.assertRaises(ValueError, next, search)
class TestSpliceGoodMAF(unittest.TestCase):
"""Test in silico splicing on a correctly-formatted MAF."""
def setUp(self):
self.idx = MafIndex(
"MAF/ucsc_mm9_chr10_big.mafindex",
"MAF/ucsc_mm9_chr10_big.maf",
"mm9.chr10",
)
self.assertEqual(len(self.idx), 983)
def test_invalid_strand(self):
self.assertRaises(
ValueError, self.idx.get_spliced, (0, 1000), (500, 1500), "."
)
def test_no_alignment(self):
result = self.idx.get_spliced((0, 1000), (500, 1500), 1)
self.assertEqual(len(result), 1)
self.assertEqual(len(result[0].seq), 1000)
self.assertEqual(str(result[0].seq), "N" * 1000)
def test_correct_retrieval_1(self):
"""Correct retrieval of Cnksr3 in mouse.
This is the real thing. We're pulling the spliced alignment of
an actual gene (Cnksr3) in mouse. It should perfectly match the
spliced transcript pulled independently from UCSC.
"""
result = self.idx.get_spliced(
(
3134303,
3185733,
3192055,
3193589,
3203538,
3206102,
3208126,
3211424,
3211872,
3217393,
3219697,
3220356,
3225954,
),
(
3134909,
3185897,
3192258,
3193677,
3203580,
3206222,
3208186,
3211493,
3212019,
3217518,
3219906,
3220446,
3227479,
),
1,
)
cnksr3 = str(SeqIO.read("MAF/cnksr3.fa", "fasta").seq).upper()
mm9_seq = "".join(
[str(x.seq) for x in result if x.id.startswith("mm9")]
).replace("-", "")
self.assertEqual(mm9_seq, cnksr3)
class TestSpliceBadMAF(unittest.TestCase):
"""Test in silico splicing on an incorrectly-formatted MAF."""
def setUp(self):
self.idx = MafIndex(
"MAF/ucsc_mm9_chr10_bad.mafindex",
"MAF/ucsc_mm9_chr10_bad.maf",
"mm9.chr10",
)
self.assertEqual(len(self.idx), 48)
def test_inconsistent_strand(self):
self.assertRaises(
ValueError, self.idx.get_spliced, (0, 3021421), (1000, 3022000), 1
)
def test_bundle_without_target(self):
self.assertRaises(
ValueError, self.idx.get_spliced, (3009319,), (3009900,), 1
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
