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
737
738
739
740
741
742
|
# 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.
"""Tests for mapping pairwise alignments."""
import os
import random
import unittest
try:
import numpy
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install numpy if you want to use Bio.Align.Alignment.map."
) from None
from Bio.Seq import Seq
from Bio.Align import PairwiseAligner
class TestSimple(unittest.TestCase):
def setUp(self):
aligner = PairwiseAligner()
aligner.internal_open_gap_score = -1
aligner.internal_extend_gap_score = -0.0
aligner.match_score = +1
aligner.mismatch_score = -1
aligner.mode = "local"
self.aligner = aligner
def test_internal(self):
aligner = self.aligner
chromosome = Seq("AAAAAAAAAAAAGGGGGGGCCCCCGGGGGGAAAAAAAAAA")
chromosome.id = "chromosome"
transcript = Seq("GGGGGGGCCCCCGGGGGGA")
transcript.id = "transcript"
sequence = Seq("GGCCCCCGGG")
sequence.id = "sequence"
alignments1 = aligner.align(chromosome, transcript)
self.assertEqual(len(alignments1), 1)
alignment1 = alignments1[0]
self.assertTrue(
numpy.array_equal(alignment1.coordinates, numpy.array([[12, 31], [0, 19]]))
)
self.assertEqual(
str(alignment1),
"""\
chromosom 12 GGGGGGGCCCCCGGGGGGA 31
0 ||||||||||||||||||| 19
transcrip 0 GGGGGGGCCCCCGGGGGGA 19
""",
)
alignments2 = aligner.align(transcript, sequence)
self.assertEqual(len(alignments2), 1)
alignment2 = alignments2[0]
self.assertTrue(
numpy.array_equal(alignment2.coordinates, numpy.array([[5, 15], [0, 10]]))
)
self.assertEqual(
str(alignment2),
"""\
transcrip 5 GGCCCCCGGG 15
0 |||||||||| 10
sequence 0 GGCCCCCGGG 10
""",
)
alignment = alignment1.map(alignment2)
self.assertTrue(
numpy.array_equal(alignment.coordinates, numpy.array([[17, 27], [0, 10]]))
)
self.assertEqual(
str(alignment),
"""\
chromosom 17 GGCCCCCGGG 27
0 |||||||||| 10
sequence 0 GGCCCCCGGG 10
""",
)
line = format(alignment, "psl")
self.assertEqual(
line,
"""\
10 0 0 0 0 0 0 0 + sequence 10 0 10 chromosome 40 17 27 1 10, 0, 17,
""",
)
def test_left_overhang(self):
aligner = self.aligner
chromosome = Seq("GGGCCCCCGGGGGGAAAAAAAAAA")
chromosome.id = "chromosome"
transcript = Seq("AGGGGGCCCCCGGGGGGA")
transcript.id = "transcript"
sequence = Seq("GGGGGCCCCCGGG")
sequence.id = "sequence"
alignments1 = aligner.align(chromosome, transcript)
self.assertEqual(len(alignments1), 1)
alignment1 = alignments1[0]
self.assertEqual(
str(alignment1),
"""\
chromosom 0 GGGCCCCCGGGGGGA 15
0 ||||||||||||||| 15
transcrip 3 GGGCCCCCGGGGGGA 18
""",
)
alignments2 = aligner.align(transcript, sequence)
self.assertEqual(len(alignments2), 1)
alignment2 = alignments2[0]
self.assertEqual(
str(alignment2),
"""\
transcrip 1 GGGGGCCCCCGGG 14
0 ||||||||||||| 13
sequence 0 GGGGGCCCCCGGG 13
""",
)
alignment = alignment1.map(alignment2)
self.assertTrue(
numpy.array_equal(alignment.coordinates, numpy.array([[0, 11], [2, 13]]))
)
self.assertEqual(
str(alignment),
"""\
chromosom 0 GGGCCCCCGGG 11
0 ||||||||||| 11
sequence 2 GGGCCCCCGGG 13
""",
)
line = format(alignment, "psl")
self.assertEqual(
line,
"""\
11 0 0 0 0 0 0 0 + sequence 13 2 13 chromosome 24 0 11 1 11, 2, 0,
""",
)
def test_right_overhang(self):
aligner = self.aligner
chromosome = Seq("AAAAAAAAAAAAGGGGGGGCCCCCGGG")
chromosome.id = "chromosome"
transcript = Seq("GGGGGGGCCCCCGGGGGGA")
transcript.id = "transcript"
sequence = Seq("GGCCCCCGGGGG")
sequence.id = "sequence"
alignments1 = aligner.align(chromosome, transcript)
self.assertEqual(len(alignments1), 1)
alignment1 = alignments1[0]
self.assertEqual(
str(alignment1),
"""\
chromosom 12 GGGGGGGCCCCCGGG 27
0 ||||||||||||||| 15
transcrip 0 GGGGGGGCCCCCGGG 15
""",
)
alignments2 = aligner.align(transcript, sequence)
self.assertEqual(len(alignments2), 1)
alignment2 = alignments2[0]
self.assertEqual(
str(alignment2),
"""\
transcrip 5 GGCCCCCGGGGG 17
0 |||||||||||| 12
sequence 0 GGCCCCCGGGGG 12
""",
)
alignment = alignment1.map(alignment2)
self.assertTrue(
numpy.array_equal(alignment.coordinates, numpy.array([[17, 27], [0, 10]]))
)
self.assertEqual(
str(alignment),
"""\
chromosom 17 GGCCCCCGGG 27
0 |||||||||| 10
sequence 0 GGCCCCCGGG 10
""",
)
line = format(alignment, "psl")
self.assertEqual(
line,
"""\
10 0 0 0 0 0 0 0 + sequence 12 0 10 chromosome 27 17 27 1 10, 0, 17,
""",
)
def test_reverse_transcript(self):
aligner = self.aligner
chromosome = Seq("AAAAAAAAAAAAGGGGGGGCCCCCGGGGGGAAAAAAAAAA")
chromosome.id = "chromosome"
transcript = Seq("TCCCCCCGGGGGCCCCCCC")
transcript.id = "transcript"
sequence = Seq("GGCCCCCGGG")
sequence.id = "sequence"
alignments1 = aligner.align(chromosome, transcript, strand="-")
self.assertEqual(len(alignments1), 1)
alignment1 = alignments1[0]
self.assertTrue(
numpy.array_equal(alignment1.coordinates, numpy.array([[12, 31], [19, 0]]))
)
self.assertEqual(
str(alignment1),
"""\
chromosom 12 GGGGGGGCCCCCGGGGGGA 31
0 ||||||||||||||||||| 19
transcrip 19 GGGGGGGCCCCCGGGGGGA 0
""",
)
alignments2 = aligner.align(transcript, sequence, strand="-")
self.assertEqual(len(alignments2), 1)
alignment2 = alignments2[0]
self.assertTrue(
numpy.array_equal(alignment2.coordinates, numpy.array([[4, 14], [10, 0]]))
)
self.assertEqual(
str(alignment2),
"""\
transcrip 4 CCCGGGGGCC 14
0 |||||||||| 10
sequence 10 CCCGGGGGCC 0
""",
)
alignment = alignment1.map(alignment2)
self.assertTrue(
numpy.array_equal(alignment.coordinates, numpy.array([[17, 27], [0, 10]]))
)
self.assertEqual(
str(alignment),
"""\
chromosom 17 GGCCCCCGGG 27
0 |||||||||| 10
sequence 0 GGCCCCCGGG 10
""",
)
line = format(alignment, "psl")
self.assertEqual(
line,
"""\
10 0 0 0 0 0 0 0 + sequence 10 0 10 chromosome 40 17 27 1 10, 0, 17,
""",
)
def test_reverse_sequence(self):
aligner = self.aligner
chromosome = Seq("AAAAAAAAAAAAGGGGGGGCCCCCGGGGGGAAAAAAAAAA")
chromosome.id = "chromosome"
transcript = Seq("GGGGGGGCCCCCGGGGGGA")
transcript.id = "transcript"
sequence = Seq("CCCGGGGGCC")
sequence.id = "sequence"
alignments1 = aligner.align(chromosome, transcript)
self.assertEqual(len(alignments1), 1)
alignment1 = alignments1[0]
self.assertTrue(
numpy.array_equal(alignment1.coordinates, numpy.array([[12, 31], [0, 19]]))
)
self.assertEqual(
str(alignment1),
"""\
chromosom 12 GGGGGGGCCCCCGGGGGGA 31
0 ||||||||||||||||||| 19
transcrip 0 GGGGGGGCCCCCGGGGGGA 19
""",
)
alignments2 = aligner.align(transcript, sequence, "-")
self.assertEqual(len(alignments2), 1)
alignment2 = alignments2[0]
self.assertTrue(
numpy.array_equal(alignment2.coordinates, numpy.array([[5, 15], [10, 0]]))
)
self.assertEqual(
str(alignment2),
"""\
transcrip 5 GGCCCCCGGG 15
0 |||||||||| 10
sequence 10 GGCCCCCGGG 0
""",
)
alignment = alignment1.map(alignment2)
self.assertTrue(
numpy.array_equal(alignment.coordinates, numpy.array([[17, 27], [10, 0]]))
)
self.assertEqual(
str(alignment),
"""\
chromosom 17 GGCCCCCGGG 27
0 |||||||||| 10
sequence 10 GGCCCCCGGG 0
""",
)
line = format(alignment, "psl")
self.assertEqual(
line,
"""\
10 0 0 0 0 0 0 0 - sequence 10 0 10 chromosome 40 17 27 1 10, 0, 17,
""",
)
def test_reverse_transcript_sequence(self):
aligner = self.aligner
chromosome = Seq("AAAAAAAAAAAAGGGGGGGCCCCCGGGGGGAAAAAAAAAA")
chromosome.id = "chromosome"
transcript = Seq("TCCCCCCGGGGGCCCCCCC")
transcript.id = "transcript"
sequence = Seq("CCCGGGGGCC")
sequence.id = "sequence"
alignments1 = aligner.align(chromosome, transcript, "-")
self.assertEqual(len(alignments1), 1)
alignment1 = alignments1[0]
self.assertTrue(
numpy.array_equal(alignment1.coordinates, numpy.array([[12, 31], [19, 0]]))
)
self.assertEqual(
str(alignment1),
"""\
chromosom 12 GGGGGGGCCCCCGGGGGGA 31
0 ||||||||||||||||||| 19
transcrip 19 GGGGGGGCCCCCGGGGGGA 0
""",
)
alignments2 = aligner.align(transcript, sequence)
self.assertEqual(len(alignments2), 1)
alignment2 = alignments2[0]
self.assertTrue(
numpy.array_equal(alignment2.coordinates, numpy.array([[4, 14], [0, 10]]))
)
self.assertEqual(
str(alignment2),
"""\
transcrip 4 CCCGGGGGCC 14
0 |||||||||| 10
sequence 0 CCCGGGGGCC 10
""",
)
alignment = alignment1.map(alignment2)
self.assertTrue(
numpy.array_equal(alignment.coordinates, numpy.array([[17, 27], [10, 0]]))
)
self.assertEqual(
str(alignment),
"""\
chromosom 17 GGCCCCCGGG 27
0 |||||||||| 10
sequence 10 GGCCCCCGGG 0
""",
)
line = format(alignment, "psl")
self.assertEqual(
line,
"""\
10 0 0 0 0 0 0 0 - sequence 10 0 10 chromosome 40 17 27 1 10, 0, 17,
""",
)
class TestComplex(unittest.TestCase):
def setUp(self):
aligner = PairwiseAligner()
aligner.internal_open_gap_score = -1
aligner.internal_extend_gap_score = -0.0
aligner.match_score = +1
aligner.mismatch_score = -1
aligner.mode = "local"
self.aligner = aligner
def test1(self):
aligner = self.aligner
chromosome = Seq(
"GCCTACCGTATAACAATGGTTATAATACAAGGCGGTCATAATTAAAGGGAGTGCAGCAACGGCCTGCTCTCCAAAAAAACAGGTTTTATGAAAAGAAAGTGCATTAACTGTTAAAGCCGTCATATCGGTGGGTTCTGCCAGTCACCGGCATACGTCCTGGGACAAAGACTTTTTACTACAATGCCAGGCGGGAGAGTCACCCGCCGCGGTGTCGACCCAGGGGACAGCGGGAAGATGTCGTGGTTTCCTTGTCATTAACCAACTCCATCTTAAAAGCTCCTCTAGCCATGGCATGGTACGTTGCGCGCACCCTTTTATCGGTAAGGCGCGGTGACTCTCTCCCAAAACAGTGCCATAATGGTTCGCTTCCTACCTAAGGCACTTACGGCCAATTAATGCGCAAGCGAGCGGAAGGTCTAACAGGGCACCGAATTCGATTA"
)
chromosome.id = "chromosome"
transcript = Seq(
"GGAATTTTAGCAGCCAAAGGACGGATCCTCCAAGGGGCCCCAGCACAGCACATTTTTAACGCGAACTAAGCGGGAGCGCATGTGGGACAGTTGATCCCATCCGCCTCAAAATTTCTCGCAATATCGGTTGGGGCACAGGTCCACTTTACGAATTCATACCGTGGTAGAGACCTTTATTAGATAGATATGACTGTTTGATTGCGGCATAGTACGACGAAGCAAGGGGATGGACGTTTCGGTTGCATTCGACCGGGTTGGGTCGAAAAACAGGTTTTATGAAAAGAAAGTGCATTAACTGTTAAAGCCGTCATATCGGTGGGTTC"
)
transcript.id = "transcript"
sequence = Seq(
"TCCAAGGGGCCCCAGCACAGCACATTTTTAACGCGGGGACAGTTGATCCCATCCGCCTTTTACGAATTCATACCGTGGTAGGCGGCATAGTACGACGAAGCGGTTGGGTCGAAAAACAGGTTGCCGTCATATCGGTGGGTTC"
)
sequence.id = "sequence"
alignments1 = aligner.align(chromosome, transcript)
alignment1 = alignments1[0]
self.assertEqual(alignment1.coordinates.shape[1], 164)
self.assertEqual(
str(alignment1),
"""\
chromosom 14 AATGGTTATA------ATACAAGG-CGG----TCATAATTAAAGGGAGTG---CAGCAAC
0 |||--||-||------|---||||-|||----||------.|||||---|---|||||--
transcrip 2 AAT--TT-TAGCAGCCA---AAGGACGGATCCTC------CAAGGG---GCCCCAGCA--
chromosom 60 GGCCTGCTCTCCAAAAAAACAGGTTTTATGAAAAGAAAGTGCATTAACTGTTAAAGC---
60 ---|.||-----------|||--||||-|------||.|.|----||||----||||---
transcrip 45 ---CAGC-----------ACA--TTTT-T------AACGCG----AACT----AAGCGGG
chromosom 117 --CGTCATATCGGTGG----GTTCTGCCAGTCACCGGCATACGTCCTGGGACAAAGACTT
120 --||-|||----||||----||--||--|-|--||--|||.||-|||----||||-|---
transcrip 74 AGCG-CAT----GTGGGACAGT--TG--A-T--CC--CATCCG-CCT----CAAA-A---
chromosom 171 TTTACT-ACAATGCCAGGCGGGAGAGTCACCCGCCGCGGTGTCGACCCAGGGG-ACAGCG
180 |||-||-.||||------------|-|---------||||-|-------||||-||||--
transcrip 111 TTT-CTCGCAAT------------A-T---------CGGT-T-------GGGGCACAG--
chromosom 229 GGAAGATGTCGTGGTTTC-CTT---G---TCATTAACC-------A-ACTCCATCTTA--
240 -------|||-------|-|||---|---||||--|||-------|-|--||-|-|||--
transcrip 138 -------GTC-------CACTTTACGAATTCAT--ACCGTGGTAGAGA--CC-T-TTATT
chromosom 272 AAAGCTCCTCTAGCCATGGCATG---GT---ACGTTGCGCGCACCCTTTTA-T----CG-
300 |.|-------|||--||---|||---||---|--|||||-|||------||-|----||-
transcrip 178 AGA-------TAG--AT---ATGACTGTTTGA--TTGCG-GCA------TAGTACGACGA
chromosom 320 -GTAAGG-------CG---CGGT-------GACTCTC--------TCCCAAAACAGTGCC
360 -|.||||-------||---||||-------|||---|--------||..||||||-----
transcrip 217 AGCAAGGGGATGGACGTTTCGGTTGCATTCGAC---CGGGTTGGGTCGAAAAACA-----
chromosom 354 ATAATGGTTCGCTTCCTACCT-------AAG-GCACTT-ACGGCCAATTAATGCGCAAGC
420 -----|||----||--||--|-------|||-|||-||-||.|----|||------||||
transcrip 269 -----GGT----TT--TA--TGAAAAGAAAGTGCA-TTAACTG----TTA------AAGC
chromosom 405 GAGCGGAAGGTC-TAACAG-GGCACCGAATTC 435
480 ---|-----|||-||.|.|-||----|--||| 512
transcrip 305 ---C-----GTCATATCGGTGG----G--TTC 323
""",
)
alignments2 = aligner.align(transcript, sequence)
alignment2 = alignments2[0]
self.assertEqual(alignment2.coordinates.shape[1], 12)
self.assertEqual(
str(alignment2),
"""\
transcrip 28 TCCAAGGGGCCCCAGCACAGCACATTTTTAACGCGAACTAAGCGGGAGCGCATGTGGGAC
0 |||||||||||||||||||||||||||||||||||--------------------|||||
sequence 0 TCCAAGGGGCCCCAGCACAGCACATTTTTAACGCG--------------------GGGAC
transcrip 88 AGTTGATCCCATCCGCCTCAAAATTTCTCGCAATATCGGTTGGGGCACAGGTCCACTTTA
60 ||||||||||||||||||--------------------------------------||||
sequence 40 AGTTGATCCCATCCGCCT--------------------------------------TTTA
transcrip 148 CGAATTCATACCGTGGTAGAGACCTTTATTAGATAGATATGACTGTTTGATTGCGGCATA
120 |||||||||||||||||||---------------------------------||||||||
sequence 62 CGAATTCATACCGTGGTAG---------------------------------GCGGCATA
transcrip 208 GTACGACGAAGCAAGGGGATGGACGTTTCGGTTGCATTCGACCGGGTTGGGTCGAAAAAC
180 ||||||||||||--------------------------------||||||||||||||||
sequence 89 GTACGACGAAGC--------------------------------GGTTGGGTCGAAAAAC
transcrip 268 AGGTTTTATGAAAAGAAAGTGCATTAACTGTTAAAGCCGTCATATCGGTGGGTTC 323
240 |||||------------------------------|||||||||||||||||||| 295
sequence 117 AGGTT------------------------------GCCGTCATATCGGTGGGTTC 142
""",
)
alignment = alignment1.map(alignment2)
self.assertEqual(alignment.coordinates.shape[1], 76)
self.assertEqual(
str(alignment),
"""\
chromosom 35 TCATAATTAAAGGGAGTG---CAGCAACGGCCTGCTCTCCAAAAAAACAGGTTTTATGAA
0 ||------.|||||---|---|||||-----|.||-----------|||--||||-|---
sequence 0 TC------CAAGGG---GCCCCAGCA-----CAGC-----------ACA--TTTT-T---
chromosom 92 AAGAAAGTGCATTAACTGTTAAAGCCGTCATATCGGTGG----GTTCTGCCAGTCACCGG
60 ---||.|.|----------------------------||----||--||--|-|--||--
sequence 29 ---AACGCG----------------------------GGGACAGT--TG--A-T--CC--
chromosom 148 CATACGTCCTGGGACAAAGACTTTTTACTACAATGCCAGGCGGGAGAGTCACCCGCCGCG
120 |||.||-|||--------------------------------------------------
sequence 49 CATCCG-CCT--------------------------------------------------
chromosom 208 GTGTCGACCCAGGGGACAGCGGGAAGATGTCGTGGTTTCCTT---G---TCATTAACCAA
180 ----------------------------------------||---|---||||--|||--
sequence 58 ----------------------------------------TTTACGAATTCAT--ACC--
chromosom 262 CTCCATCTTAAAAGCTCCTCTAGCCATGGCATGGTACGTT-------GCGCGCACCCTTT
240 -----------------------------------------------|||-|||------
sequence 74 ----------------------------------------GTGGTAGGCG-GCA------
chromosom 315 TA-T----CG--GTAAGGCGCGGTGACTCTC-------TCCCAAAACAGTGCCATAATGG
300 ||-|----||--|.------------------------||..||||||----------||
sequence 87 TAGTACGACGAAGC-----------------GGTTGGGTCGAAAAACA----------GG
chromosom 361 TTCGCTTCCTACCTAAGGCACTTACGGCCAATTAATGCGCAAGCGAGCGGAAGGTC-TAA
360 |----|------------------------------------||---|-----|||-||.
sequence 120 T----T------------------------------------GC---C-----GTCATAT
chromosom 420 CAG-GGCACCGAATTC 435
420 |.|-||----|--||| 436
sequence 132 CGGTGG----G--TTC 142
""",
)
line = format(alignment, "psl")
self.assertEqual(
line,
"""\
96 10 0 0 11 36 27 294 + sequence 142 0 142 chromosome 440 35 435 37 2,6,1,5,4,3,4,1,6,2,2,2,1,1,2,6,3,2,1,4,3,3,3,2,1,2,2,10,3,1,2,1,3,6,2,1,3, 0,2,8,12,17,21,24,28,29,35,41,43,45,46,47,49,55,58,63,67,71,81,84,87,90,95,99,108,118,121,122,124,125,129,136,138,139, 35,43,52,53,63,78,83,88,95,129,131,135,139,141,144,148,155,248,250,251,257,302,306,315,317,318,320,339,359,366,403,408,414,417,423,429,432,
""",
)
def test2(self):
aligner = self.aligner
chromosome = Seq(
"CTAATGCGCCTTGGTTTTGGCTTAACTAGAAGCAACCTGTAAGATTGCCAATTCTTCAGTCGAAGTAAATCTTCAATGTTTTGGACTCTTAGCGGATATGCGGCTGAGAAGTACGACATGTGTACATTCATACCTGCGTGACGGTCAGCCTCCCCCGGGACCTCATTGGGCGAATCTAGGTGTGATAATTGACACACTCTTGGTAAGAAGCACTCTTTACCCGATCTCCAAGTACCGACGCCAAGGCCAAGCTCTGCGATCTAAAGCTGCCGATCGTAGATCCAAGTCCTCAGCAAGCTCGCACGAATACGCAGTTCGAAGGCTGGGTGTTGTACGACGGTACGGTTGCTATAGCACTTTCGCGGTCTCGCTATTTTCAGTTTGACTCACCAGTCAGTATTGTCATCGACCAACTTGGAATAGTGTAACGCAGCGCTTGA"
)
chromosome.id = "chromosome"
transcript = Seq(
"CACCGGCGTCGGTACCAGAGGGCGTGAGTACCTTGTACTAGTACTCATTGGAATAATGCTCTTAGAAGTCATCTAAAAGTGACAACGCCTGTTTGGTTATGACGTTCACGACGCGTCTTAACAGACTAGCATTAGACCGACGGGTTGAGGCGTCTGGGTTGATACAGCCGTTTGCATCAGTGTATCTAACACTCTGAGGGATAATTGATGAACCGTGTTTTCCGATAGGTATGTACAGTACCACCACGCACGACTAAGGACCATTTTCTGCGTGCGACGGTTAAAATAACCTCAATCACT"
)
transcript.id = "transcript"
sequence = Seq(
"TCCCCTTCTAATGGAATCCCCCTCCGAAGGTCGCAGAAGCGGCCACGCCGGAGATACCAGTTCCACGCCTCAGGTTGGACTTGTCACACTTGTACGCGAT"
)
sequence.id = "sequence"
alignments1 = aligner.align(chromosome, transcript)
alignment1 = alignments1[0]
self.assertEqual(alignment1.coordinates.shape[1], 126)
self.assertEqual(
str(alignment1),
"""\
chromosom 5 GCGCCTTGGTTTTGGCTTAACTAGA-------AGCAACC-TGTAAGATTGCCAATTCTTC
0 |||--|.|||---------||.|||-------||-.|||-||||------------||--
transcrip 5 GCG--TCGGT---------ACCAGAGGGCGTGAG-TACCTTGTA------------CT--
chromosom 57 AGTCGAAGTAAATCTTCAATGTTTTGGA------CTCTTAG----CGGATATGCGGCTGA
60 ------||||---|-|||-----|||||------|||||||----|----||----||-|
transcrip 39 ------AGTA---C-TCA-----TTGGAATAATGCTCTTAGAAGTC----AT----CT-A
chromosom 107 GAAGTACGACA-----TGT---GT----ACATTCATAC--CTGCGT-------GACGGTC
120 .||||--||||-----|||---||----||.|||--||--|-||||-------|||--|-
transcrip 75 AAAGT--GACAACGCCTGTTTGGTTATGACGTTC--ACGAC-GCGTCTTAACAGAC--T-
chromosom 146 AGCCT----CCCCCGGGACCTCATTG-GGCGAATCTAGGTGTGATA-A-----TTGACA-
180 |||.|----||..||||------|||-||||--|||.|||-|||||-|-----|||-||-
transcrip 127 AGCATTAGACCGACGGG------TTGAGGCG--TCTGGGT-TGATACAGCCGTTTG-CAT
chromosom 194 CA----CTCTTGGTAAGAAGCACTCT---------TTACCCGATCTCCAAGTACCGACGC
240 ||----.|||-------||-||||||---------||----|||------|.||||----
transcrip 177 CAGTGTATCT-------AA-CACTCTGAGGGATAATT----GAT------GAACCG----
chromosom 241 CAAGGCCAAGCTCTG-----CGATCTAAAGCTGCCGATCGTAGATCCAAGTCCTCAGCAA
300 -------------||-----||||----||.|----||-|||----|-|||.|-||.||-
transcrip 215 -------------TGTTTTCCGAT----AGGT----AT-GTA----C-AGTAC-CACCA-
chromosom 296 GCTCGCACGAATACGCAG-------TTCGAAGGCTGGGTGTTGTACGACGGTACGGTTGC
360 ---|||||||.||---||-------||------|||.|||-----|||||||--------
transcrip 246 ---CGCACGACTA---AGGACCATTTT------CTGCGTG-----CGACGGT--------
chromosom 349 TATAGCACTTTCGCGGTCTCGCTATTTTCAGTTTGACTCACCAGTCAGTATTGTCATCGA
420 ||-|--|----------------||----------|---|||--|||--------|||--
transcrip 281 TA-A--A----------------AT----------A---ACC--TCA--------ATC--
chromosom 409 CCAACT 415
480 ---||| 486
transcrip 297 ---ACT 300
""",
)
alignments2 = aligner.align(transcript, sequence)
alignment2 = alignments2[0]
self.assertEqual(alignment2.coordinates.shape[1], 66)
self.assertEqual(
str(alignment2),
"""\
transcrip 8 TCGGTACCAGAGGGCGTGAGTACCTTGTACTAGTACTCATTGGAATAATGCTCTTAGAAG
0 ||------------|-------||||---|||------|-||||||--------------
sequence 0 TC------------C-------CCTT---CTA------A-TGGAAT--------------
transcrip 68 TCATCTAAAAGTGACAACGCCTGTTTGGTTATGACGTTCACGACGCGTCTTAACAGACTA
60 -----------------|.||-------------|--||-|||.|-|||---.||||--|
sequence 17 -----------------CCCC-------------C--TC-CGAAG-GTC---GCAGA--A
transcrip 128 GCATTAGACCGACG--GGTTGAGGCGTCTGGGTTGATACAGCCGTTTGCATCAGTGTATC
120 ||----|.||-|||--|---||------------|||||------------||||---||
sequence 38 GC----GGCC-ACGCCG---GA------------GATAC------------CAGT---TC
transcrip 186 TAACA---CTCTGAGGGATAATTGATGAACCGTGTTTTCCGATAGGTATGTACAGTACCA
180 ---||---|||--|||-----|||--||--|-----||----------------||----
sequence 63 ---CACGCCTC--AGG-----TTG--GA--C-----TT----------------GT----
transcrip 243 CCACGCACGACTAAGGACCATTTTCTG--CGTGCGA 277
240 -----|||-|||-------------||--|--|||| 276
sequence 84 -----CAC-ACT-------------TGTAC--GCGA 99
""",
)
alignment = alignment1.map(alignment2)
self.assertEqual(alignment.coordinates.shape[1], 78)
self.assertEqual(
str(alignment),
"""\
chromosom 10 TTGGTTTTGGCTTAACTAGAAGCAA-CC-TGTAAGATTGCCAATTCTTCAGTCGAAGTAA
0 |.------------------------||-|---------------||--------|----
sequence 0 TC-----------------------CCCTT---------------CT--------A----
chromosom 68 ATCTTCAATGTTTTGGACTCTTAGCGGATATGCGGCTGAGAAGTACGACATGTGTA----
60 ------|------||||-------------------------------------------
sequence 10 ------A------TGGA---------------------------------------ATCC
chromosom 124 --CATTCATAC--CTGCGT----GACGGTCAGCCT--CCCCCG--GGACCTCATTGGGCG
120 --|--||---|--.-|-||----||-----|||----||-.||--|---------|----
sequence 19 CCC--TC---CGAA-G-GTCGCAGA-----AGC--GGCC-ACGCCG---------G----
chromosom 172 AATCTAGGTGT-GATAATTGACA-CAC--TCTTGGTAAGAAGCA---CTCT---TTACCC
180 ------------||||--------||---||-----------||---|||----||----
sequence 51 -----------AGATA-------CCA-GTTC-----------CACGCCTC-AGGTT----
chromosom 222 GATCTCCAAGTACCGACGCCAAGGCCAAGCTCTGCGATCTAAAGCTGCCGATCGTAGATC
240 |--------|.--|----------------------------------------------
sequence 76 G--------GA--C----------------------------------------------
chromosom 282 CAA--GTCCTCAGCAAGCTCGCACGAATACGCAGTTCGAAGGCTG--GGTGTTGTACGA
300 -----||--------------|||-|.|---------------||--.--|-----|||
sequence 80 ---TTGT--------------CAC-ACT---------------TGTAC--G-----CGA
chromosom 337
359
sequence 99
""",
)
line = format(alignment, "psl")
self.assertEqual(
line,
"""\
61 6 0 0 14 32 28 260 + sequence 100 0 99 chromosome 440 10 337 35 2,2,1,2,1,1,4,1,2,1,1,1,2,2,3,2,3,1,1,4,2,2,2,3,2,1,2,1,2,3,3,2,1,1,3, 0,3,6,7,9,10,11,21,22,24,27,28,29,35,37,42,44,49,50,52,57,61,63,68,74,76,77,79,82,84,87,90,94,95,96, 10,35,37,53,63,74,81,124,127,132,133,135,137,139,146,151,154,157,167,183,194,197,210,212,216,222,231,235,285,301,305,323,325,328,334,
""",
)
def map_check(alignment1, alignment2):
line1 = format(alignment1, "psl")
handle = open("transcript.psl", "w")
handle.write(line1)
handle.close()
line2 = format(alignment2, "psl")
handle = open("sequence.psl", "w")
handle.write(line2)
handle.close()
stdout = os.popen("pslMap sequence.psl transcript.psl stdout")
line = stdout.read()
os.remove("transcript.psl")
os.remove("sequence.psl")
return line
def test_random(aligner, nBlocks1=1, nBlocks2=1, strand1="+", strand2="+"):
chromosome = "".join(["ACGT"[random.randint(0, 3)] for i in range(1000)])
nBlocks = nBlocks1
transcript = ""
position = 0
for i in range(nBlocks):
position += random.randint(60, 80)
blockSize = random.randint(60, 80)
transcript += chromosome[position : position + blockSize]
position += blockSize
nBlocks = nBlocks2
sequence = ""
position = 0
for i in range(nBlocks):
position += random.randint(20, 40)
blockSize = random.randint(20, 40)
sequence += transcript[position : position + blockSize]
position += blockSize
chromosome = Seq(chromosome)
transcript = Seq(transcript)
sequence = Seq(sequence)
if strand1 == "-":
chromosome = chromosome.reverse_complement()
if strand2 == "-":
sequence = sequence.reverse_complement()
chromosome.id = "chromosome"
transcript.id = "transcript"
sequence.id = "sequence"
alignments1 = aligner.align(chromosome, transcript, strand=strand1)
alignment1 = alignments1[0]
alignments2 = aligner.align(transcript, sequence, strand=strand2)
alignment2 = alignments2[0]
alignment = alignment1.map(alignment2)
line_check = map_check(alignment1, alignment2)
line = format(alignment, "psl")
assert line == line_check
print("Randomized test %d, %d, %s, %s OK" % (nBlocks1, nBlocks2, strand1, strand2))
def test_random_sequences(aligner, strand1="+", strand2="+"):
chromosome = "".join(["ACGT"[random.randint(0, 3)] for i in range(1000)])
transcript = "".join(["ACGT"[random.randint(0, 3)] for i in range(300)])
sequence = "".join(["ACGT"[random.randint(0, 3)] for i in range(100)])
chromosome = Seq(chromosome)
transcript = Seq(transcript)
sequence = Seq(sequence)
chromosome.id = "chromosome"
transcript.id = "transcript"
sequence.id = "sequence"
alignments = aligner.align(chromosome, transcript, strand=strand1)
alignment1 = alignments[0]
alignments = aligner.align(transcript, sequence, strand=strand2)
alignment2 = alignments[0]
line_check = map_check(alignment1, alignment2)
alignment = alignment1.map(alignment2)
line_check = line_check.split()
line = format(alignment, "psl")
line = line.split()
assert line[8:] == line_check[8:]
line1 = format(alignment1, "psl")
words = line1.split()
nBlocks1 = int(words[17])
line2 = format(alignment2, "psl")
words = line2.split()
nBlocks2 = int(words[17])
print(
"Randomized sequence test %d, %d, %s, %s OK"
% (nBlocks1, nBlocks2, strand1, strand2)
)
def perform_randomized_tests(n=1000):
"""Perform randomized tests and compare to pslMap.
Run this function to perform 8 x n mappings for alignments of randomly
generated sequences, get the alignment in PSL format, and compare the
result to that of pslMap.
"""
aligner = PairwiseAligner()
aligner.internal_open_gap_score = -1
aligner.internal_extend_gap_score = -0.0
aligner.match_score = +1
aligner.mismatch_score = -1
aligner.mode = "local"
for i in range(n):
nBlocks1 = random.randint(1, 10)
nBlocks2 = random.randint(1, 10)
test_random(aligner, nBlocks1, nBlocks2, "+", "+")
test_random(aligner, nBlocks1, nBlocks2, "+", "-")
test_random(aligner, nBlocks1, nBlocks2, "-", "+")
test_random(aligner, nBlocks1, nBlocks2, "-", "-")
test_random_sequences(aligner, "+", "+")
test_random_sequences(aligner, "+", "-")
test_random_sequences(aligner, "-", "+")
test_random_sequences(aligner, "-", "-")
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
|
