forked from biopython/biopython
/
test_motifs.py
1709 lines (1674 loc) · 103 KB
/
test_motifs.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
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
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
# Copyright 2008 by Bartek Wilczynski. All rights reserved.
# Adapted from test_Mymodule.py by Jeff Chang
# 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.
import os
import unittest
import math
from Bio.Alphabet import generic_dna
from Bio.Alphabet import Gapped
from Bio.Alphabet import IUPAC
from Bio import motifs
from Bio.Seq import Seq
class MotifTestsBasic(unittest.TestCase):
def setUp(self):
self.PFMin = open("motifs/SRF.pfm")
self.SITESin = open("motifs/Arnt.sites")
self.TFout = "motifs/tf.out"
self.FAout = "motifs/fa.out"
self.PFMout = "motifs/fa.out"
instance = Seq("ATATA")
instances = [instance]
self.m = motifs.create(instances)
def tearDown(self):
self.PFMin.close()
self.SITESin.close()
if os.path.exists(self.TFout):
os.remove(self.TFout)
if os.path.exists(self.FAout):
os.remove(self.FAout)
def test_alignace_parsing(self):
"""Test if Bio.motifs can parse AlignAce output files.
"""
handle = open("motifs/alignace.out")
record = motifs.parse(handle, "AlignAce")
handle.close()
self.assertEqual(record.version, "AlignACE 4.0 05/13/04")
self.assertEqual(record.command, "./AlignACE -i test.fa")
self.assertEqual(len(record.parameters), 7)
self.assertEqual(record.parameters['expect'], "10")
self.assertEqual(record.parameters['gcback'], "0.38")
self.assertEqual(record.parameters['minpass'], "200")
self.assertEqual(record.parameters['seed'], "1227623309")
self.assertEqual(record.parameters['numcols'], "10")
self.assertEqual(record.parameters['undersample'], "1")
self.assertEqual(record.parameters['oversample'], "1")
self.assertEqual(len(record.sequences), 10)
self.assertEqual(record.sequences[0], "SEQ1; M: CTCAATCGTAGA at 52")
self.assertEqual(record.sequences[1], "SEQ2; M: CTCAATCGTAGA at 172")
self.assertEqual(record.sequences[2], "SEQ3; M: CTCAATCGTAGA at 112")
self.assertEqual(record.sequences[3], "SEQ4; M: CTCAATCGTAGA at 173")
self.assertEqual(record.sequences[4], "SEQ5; M: CTCAATCGTAGA at 185")
self.assertEqual(record.sequences[5], "SEQ6; M: CTCAATCGTAGA at 105")
self.assertEqual(record.sequences[6], "SEQ7; M: CTCAATCGTAGA at 177")
self.assertEqual(record.sequences[7], "SEQ8; M: CTCAATCGTAGA at 172")
self.assertEqual(record.sequences[8], "SEQ9; M: CTCAATCGTAGA at 93")
self.assertEqual(record.sequences[9], "SEQ10; M: CTCAATCGTAGA at 3")
self.assertEqual(len(record), 16)
self.assertEqual(record[0].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[0].instances), 11)
self.assertEqual(str(record[0].instances[0]), "TCTACGATTGAG")
self.assertEqual(str(record[0].instances[1]), "TCTACGATTGAG")
self.assertEqual(str(record[0].instances[2]), "TCTACGATTGAG")
self.assertEqual(str(record[0].instances[3]), "TCTACGATTGAG")
self.assertEqual(str(record[0].instances[4]), "TCTACGATTGAG")
self.assertEqual(str(record[0].instances[5]), "TCTACGATTGAG")
self.assertEqual(str(record[0].instances[6]), "TCTACGATTGAG")
self.assertEqual(str(record[0].instances[7]), "TCTACGATTGAG")
self.assertEqual(str(record[0].instances[8]), "TCTACGATTGAG")
self.assertEqual(str(record[0].instances[9]), "TCAAAGATAGAG")
self.assertEqual(str(record[0].instances[10]), "TCTACGATTGAG")
self.assertEqual(record[0].mask, (1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1))
self.assertAlmostEqual(record[0].score, 57.9079)
self.assertEqual(record[1].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[1].instances), 22)
self.assertEqual(str(record[1].instances[0]), "GCGAAGGAAGCAGCGCGTGTG")
self.assertEqual(str(record[1].instances[1]), "GGCACCGCCTCTACGATTGAG")
self.assertEqual(str(record[1].instances[2]), "CAGAGCTTAGCATTGAACGCG")
self.assertEqual(str(record[1].instances[3]), "CTAATGAAAGCAATGAGAGTG")
self.assertEqual(str(record[1].instances[4]), "CTTGTGCCCTCTAAGCGTCCG")
self.assertEqual(str(record[1].instances[5]), "GAGCACGACGCTTTGTACCTG")
self.assertEqual(str(record[1].instances[6]), "CGGCACTTAGCAGCGTATCGT")
self.assertEqual(str(record[1].instances[7]), "CTGGTTTCATCTACGATTGAG")
self.assertEqual(str(record[1].instances[8]), "GGGCCAATAGCGGCGCCGGAG")
self.assertEqual(str(record[1].instances[9]), "GTGGAGTTATCTTAGTGCGCG")
self.assertEqual(str(record[1].instances[10]), "GAGAGGTTATCTACGATTGAG")
self.assertEqual(str(record[1].instances[11]), "CTGCTCCCCGCATACAGCGCG")
self.assertEqual(str(record[1].instances[12]), "CAGAACCGAGGTCCGGTACGG")
self.assertEqual(str(record[1].instances[13]), "GTGCCCCAAGCTTACCCAGGG")
self.assertEqual(str(record[1].instances[14]), "CGCCTCTGATCTACGATTGAG")
self.assertEqual(str(record[1].instances[15]), "GTGCTCATAGGGACGTCGCGG")
self.assertEqual(str(record[1].instances[16]), "CTGCCCCCCGCATAGTAGGGG")
self.assertEqual(str(record[1].instances[17]), "GTAAAGAAATCGATGTGCCAG")
self.assertEqual(str(record[1].instances[18]), "CACCTGCAATTGCTGGCAGCG")
self.assertEqual(str(record[1].instances[19]), "GGCGGGCCATCCCTGTATGAA")
self.assertEqual(str(record[1].instances[20]), "CTCCAGGTCGCATGGAGAGAG")
self.assertEqual(str(record[1].instances[21]), "CCTCGGATCGCTTGGGAAGAG")
self.assertEqual(record[1].mask, (1, 0, 1, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 1))
self.assertAlmostEqual(record[1].score, 19.6235)
self.assertEqual(record[2].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[2].instances), 18)
self.assertEqual(str(record[2].instances[0]), "GTGCGCGAAGGAAGCAGCGCG")
self.assertEqual(str(record[2].instances[1]), "CAGAGCTTAGCATTGAACGCG")
self.assertEqual(str(record[2].instances[2]), "GTGCCCGATGACCACCCGTCG")
self.assertEqual(str(record[2].instances[3]), "GCCCTCTAAGCGTCCGCGGAT")
self.assertEqual(str(record[2].instances[4]), "GAGCACGACGCTTTGTACCTG")
self.assertEqual(str(record[2].instances[5]), "CGGCACTTAGCAGCGTATCGT")
self.assertEqual(str(record[2].instances[6]), "GGGCCAATAGCGGCGCCGGAG")
self.assertEqual(str(record[2].instances[7]), "GCGCACTAAGATAACTCCACG")
self.assertEqual(str(record[2].instances[8]), "CGGCCCGTTGTCCAGCAGACG")
self.assertEqual(str(record[2].instances[9]), "CTGCTCCCCGCATACAGCGCG")
self.assertEqual(str(record[2].instances[10]), "GTGCCCCAAGCTTACCCAGGG")
self.assertEqual(str(record[2].instances[11]), "GTGCTCATAGGGACGTCGCGG")
self.assertEqual(str(record[2].instances[12]), "CTGCCCCCCGCATAGTAGGGG")
self.assertEqual(str(record[2].instances[13]), "CGCCGCCATGCGACGCAGAGG")
self.assertEqual(str(record[2].instances[14]), "AACCTCTAAGCATACTCTACG")
self.assertEqual(str(record[2].instances[15]), "GACCTGGAGGCTTAGACTTGG")
self.assertEqual(str(record[2].instances[16]), "GCGCTCTTCCCAAGCGATCCG")
self.assertEqual(str(record[2].instances[17]), "GGGCCGTCAGCTCTCAAGTCT")
self.assertEqual(record[2].mask, (1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 1))
self.assertAlmostEqual(record[2].score, 19.1804)
self.assertEqual(record[3].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[3].instances), 16)
self.assertEqual(str(record[3].instances[0]), "GCCCCAAGCTTACCCAGGGAC")
self.assertEqual(str(record[3].instances[1]), "GCCGTCTGCTGGACAACGGGC")
self.assertEqual(str(record[3].instances[2]), "GCCGACGGGTGGTCATCGGGC")
self.assertEqual(str(record[3].instances[3]), "GCCAATAGCGGCGCCGGAGTC")
self.assertEqual(str(record[3].instances[4]), "GCCCCCCGCATAGTAGGGGGA")
self.assertEqual(str(record[3].instances[5]), "GCCCGTACCGGACCTCGGTTC")
self.assertEqual(str(record[3].instances[6]), "GCCTCATGTACCGGAAGGGAC")
self.assertEqual(str(record[3].instances[7]), "GACACGCGCCTGGGAGGGTTC")
self.assertEqual(str(record[3].instances[8]), "GCCTTTGGCCTTGGATGAGAA")
self.assertEqual(str(record[3].instances[9]), "GGCCCTCGGATCGCTTGGGAA")
self.assertEqual(str(record[3].instances[10]), "GCATGTTGGGAATCCGCGGAC")
self.assertEqual(str(record[3].instances[11]), "GACACGCGCTGTATGCGGGGA")
self.assertEqual(str(record[3].instances[12]), "GCCAGGTACAAAGCGTCGTGC")
self.assertEqual(str(record[3].instances[13]), "GCGATCAGCTTGTGGGCGTGC")
self.assertEqual(str(record[3].instances[14]), "GACAAATCGGATACTGGGGCA")
self.assertEqual(str(record[3].instances[15]), "GCACTTAGCAGCGTATCGTTA")
self.assertEqual(record[3].mask, (1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 1))
self.assertAlmostEqual(record[3].score, 18.0097)
self.assertEqual(record[4].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[4].instances), 15)
self.assertEqual(str(record[4].instances[0]), "CGGCACAGAGCTT")
self.assertEqual(str(record[4].instances[1]), "ATCCGCGGACGCT")
self.assertEqual(str(record[4].instances[2]), "CGCCTGGGAGGGT")
self.assertEqual(str(record[4].instances[3]), "CGGAAGGGACGTT")
self.assertEqual(str(record[4].instances[4]), "ACACACAGACGGT")
self.assertEqual(str(record[4].instances[5]), "TGCCAGAGAGGTT")
self.assertEqual(str(record[4].instances[6]), "AGACTGAGACGTT")
self.assertEqual(str(record[4].instances[7]), "AATCGTAGAGGAT")
self.assertEqual(str(record[4].instances[8]), "CGTCTCGTAGGGT")
self.assertEqual(str(record[4].instances[9]), "CGTCGCGGAGGAT")
self.assertEqual(str(record[4].instances[10]), "CTTCTTAGACGCT")
self.assertEqual(str(record[4].instances[11]), "CGACGCAGAGGAT")
self.assertEqual(str(record[4].instances[12]), "ATGCTTAGAGGTT")
self.assertEqual(str(record[4].instances[13]), "AGACTTGGGCGAT")
self.assertEqual(str(record[4].instances[14]), "CGACCTGGAGGCT")
self.assertEqual(record[4].mask, (1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1))
self.assertAlmostEqual(record[4].score, 16.8287)
self.assertEqual(record[5].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[5].instances), 18)
self.assertEqual(str(record[5].instances[0]), "GTGCGCGAAGGAAGCAGCGCGTG")
self.assertEqual(str(record[5].instances[1]), "TTGAGCCGAGTAAAGGGCTGGTG")
self.assertEqual(str(record[5].instances[2]), "CAATGCTAAGCTCTGTGCCGACG")
self.assertEqual(str(record[5].instances[3]), "CAACTCTCTATGTAGTGCCCGAG")
self.assertEqual(str(record[5].instances[4]), "CGACGCTTTGTACCTGGCTTGCG")
self.assertEqual(str(record[5].instances[5]), "CGAGTCAATGACACGCGCCTGGG")
self.assertEqual(str(record[5].instances[6]), "CGATACGCTGCTAAGTGCCGTCC")
self.assertEqual(str(record[5].instances[7]), "CCGGGCCAATAGCGGCGCCGGAG")
self.assertEqual(str(record[5].instances[8]), "CCACGCTTCGACACGTGGTATAG")
self.assertEqual(str(record[5].instances[9]), "CCGAGCCTCATGTACCGGAAGGG")
self.assertEqual(str(record[5].instances[10]), "CTGCTCCCCGCATACAGCGCGTG")
self.assertEqual(str(record[5].instances[11]), "CCGAGGTCCGGTACGGGCAAGCC")
self.assertEqual(str(record[5].instances[12]), "GTGCTCATAGGGACGTCGCGGAG")
self.assertEqual(str(record[5].instances[13]), "CCCTACTATGCGGGGGGCAGGTC")
self.assertEqual(str(record[5].instances[14]), "GCCAGCAATTGCAGGTGGTCGTG")
self.assertEqual(str(record[5].instances[15]), "CTCTGCGTCGCATGGCGGCGTGG")
self.assertEqual(str(record[5].instances[16]), "GGAGGCTTAGACTTGGGCGATAC")
self.assertEqual(str(record[5].instances[17]), "GCATGGAGAGAGATCCGGAGGAG")
self.assertEqual(record[5].mask, (1, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 1))
self.assertAlmostEqual(record[5].score, 15.0441)
self.assertEqual(record[6].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[6].instances), 20)
self.assertEqual(str(record[6].instances[0]), "GCGCGTGTGTGTAAC")
self.assertEqual(str(record[6].instances[1]), "GCACAGAGCTTAGCA")
self.assertEqual(str(record[6].instances[2]), "GGTGGTCATCGGGCA")
self.assertEqual(str(record[6].instances[3]), "GCGCGTGTCATTGAC")
self.assertEqual(str(record[6].instances[4]), "GGACGGCACTTAGCA")
self.assertEqual(str(record[6].instances[5]), "GCGCGTCCCGGGCCA")
self.assertEqual(str(record[6].instances[6]), "GCTCGGCCCGTTGTC")
self.assertEqual(str(record[6].instances[7]), "GCGCGTGTCCTTTAA")
self.assertEqual(str(record[6].instances[8]), "GCTGATCGCTGCTCC")
self.assertEqual(str(record[6].instances[9]), "GCCCGTACCGGACCT")
self.assertEqual(str(record[6].instances[10]), "GGACGTCGCGGAGGA")
self.assertEqual(str(record[6].instances[11]), "GCGGGGGGCAGGTCA")
self.assertEqual(str(record[6].instances[12]), "GGACGTACTGGCACA")
self.assertEqual(str(record[6].instances[13]), "GCAGGTGGTCGTGCA")
self.assertEqual(str(record[6].instances[14]), "GCGCATACCTTAACA")
self.assertEqual(str(record[6].instances[15]), "GCACGGGACTTCAAC")
self.assertEqual(str(record[6].instances[16]), "GCACGTAGCTGGTAA")
self.assertEqual(str(record[6].instances[17]), "GCTCGTCTATGGTCA")
self.assertEqual(str(record[6].instances[18]), "GCGCATGCTGGATCC")
self.assertEqual(str(record[6].instances[19]), "GGCCGTCAGCTCTCA")
self.assertEqual(record[6].mask, (1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1))
self.assertAlmostEqual(record[6].score, 13.3145)
self.assertEqual(record[7].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[7].instances), 20)
self.assertEqual(str(record[7].instances[0]), "GAACCGAGGTCCGGTACGGGC")
self.assertEqual(str(record[7].instances[1]), "GCCCCCCGCATAGTAGGGGGA")
self.assertEqual(str(record[7].instances[2]), "GTCCCTGGGTAAGCTTGGGGC")
self.assertEqual(str(record[7].instances[3]), "ACTCCACGCTTCGACACGTGG")
self.assertEqual(str(record[7].instances[4]), "ATCCTCTGCGTCGCATGGCGG")
self.assertEqual(str(record[7].instances[5]), "GTTCAATGCTAAGCTCTGTGC")
self.assertEqual(str(record[7].instances[6]), "GCTCATAGGGACGTCGCGGAG")
self.assertEqual(str(record[7].instances[7]), "GTCCCGGGCCAATAGCGGCGC")
self.assertEqual(str(record[7].instances[8]), "GCACTTAGCAGCGTATCGTTA")
self.assertEqual(str(record[7].instances[9]), "GGCCCTCGGATCGCTTGGGAA")
self.assertEqual(str(record[7].instances[10]), "CTGCTGGACAACGGGCCGAGC")
self.assertEqual(str(record[7].instances[11]), "GGGCACTACATAGAGAGTTGC")
self.assertEqual(str(record[7].instances[12]), "AGCCTCCAGGTCGCATGGAGA")
self.assertEqual(str(record[7].instances[13]), "AATCGTAGATCAGAGGCGAGA")
self.assertEqual(str(record[7].instances[14]), "GAACTCCACTAAGACTTGAGA")
self.assertEqual(str(record[7].instances[15]), "GAGCAGCGATCAGCTTGTGGG")
self.assertEqual(str(record[7].instances[16]), "GCCAGGTACAAAGCGTCGTGC")
self.assertEqual(str(record[7].instances[17]), "AGTCAATGACACGCGCCTGGG")
self.assertEqual(str(record[7].instances[18]), "GGTCATGGAATCTTATGTAGC")
self.assertEqual(str(record[7].instances[19]), "GTAGATAACAGAGGTCGGGGG")
self.assertEqual(record[7].mask, (1, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1))
self.assertAlmostEqual(record[7].score, 11.6098)
self.assertEqual(record[8].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[8].instances), 14)
self.assertEqual(str(record[8].instances[0]), "CCGAGTAAAGGGCTG")
self.assertEqual(str(record[8].instances[1]), "GTGGTCATCGGGCAC")
self.assertEqual(str(record[8].instances[2]), "GATAACAGAGGTCGG")
self.assertEqual(str(record[8].instances[3]), "CGGCGCCGGAGTCTG")
self.assertEqual(str(record[8].instances[4]), "GCGCGTCCCGGGCCA")
self.assertEqual(str(record[8].instances[5]), "CTGGACAACGGGCCG")
self.assertEqual(str(record[8].instances[6]), "CGGATACTGGGGCAG")
self.assertEqual(str(record[8].instances[7]), "GGGAGCAGCGATCAG")
self.assertEqual(str(record[8].instances[8]), "CAGAACCGAGGTCCG")
self.assertEqual(str(record[8].instances[9]), "GGGTCCCTGGGTAAG")
self.assertEqual(str(record[8].instances[10]), "GTGCTCATAGGGACG")
self.assertEqual(str(record[8].instances[11]), "GAGATCCGGAGGAGG")
self.assertEqual(str(record[8].instances[12]), "GCGATCCGAGGGCCG")
self.assertEqual(str(record[8].instances[13]), "GAGTTCACATGGCTG")
self.assertEqual(record[8].mask, (1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1))
self.assertAlmostEqual(record[8].score, 11.2943)
self.assertEqual(record[9].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[9].instances), 18)
self.assertEqual(str(record[9].instances[0]), "TAGAGGCGGTG")
self.assertEqual(str(record[9].instances[1]), "GCTAAGCTCTG")
self.assertEqual(str(record[9].instances[2]), "TGGAAGCAGTG")
self.assertEqual(str(record[9].instances[3]), "GCGAGGCTGTG")
self.assertEqual(str(record[9].instances[4]), "ACGACGCTTTG")
self.assertEqual(str(record[9].instances[5]), "GGGACGCGCAC")
self.assertEqual(str(record[9].instances[6]), "TCGAAGCGTGG")
self.assertEqual(str(record[9].instances[7]), "TGTATGCGGGG")
self.assertEqual(str(record[9].instances[8]), "GGTAAGCTTGG")
self.assertEqual(str(record[9].instances[9]), "TGTACGCTGGG")
self.assertEqual(str(record[9].instances[10]), "ACTATGCGGGG")
self.assertEqual(str(record[9].instances[11]), "GGTATGCGCTG")
self.assertEqual(str(record[9].instances[12]), "GGTACCCGGAG")
self.assertEqual(str(record[9].instances[13]), "GCGACGCAGAG")
self.assertEqual(str(record[9].instances[14]), "TGGCGGCGTGG")
self.assertEqual(str(record[9].instances[15]), "TCTAGGCGGGC")
self.assertEqual(str(record[9].instances[16]), "AGTATGCTTAG")
self.assertEqual(str(record[9].instances[17]), "TGGAGGCTTAG")
self.assertEqual(record[9].mask, (1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1))
self.assertAlmostEqual(record[9].score, 9.7924)
self.assertEqual(record[10].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[10].instances), 13)
self.assertEqual(str(record[10].instances[0]), "GCACAGAGCTTAGCATTGAAC")
self.assertEqual(str(record[10].instances[1]), "GTCCGCGGATTCCCAACATGC")
self.assertEqual(str(record[10].instances[2]), "ATACACAGCCTCGCAAGCCAG")
self.assertEqual(str(record[10].instances[3]), "GGCCCGGGACGCGCACTAAGA")
self.assertEqual(str(record[10].instances[4]), "GCCCGTTGTCCAGCAGACGGC")
self.assertEqual(str(record[10].instances[5]), "GAGCAGCGATCAGCTTGTGGG")
self.assertEqual(str(record[10].instances[6]), "GAACCGAGGTCCGGTACGGGC")
self.assertEqual(str(record[10].instances[7]), "GTCCCTGGGTAAGCTTGGGGC")
self.assertEqual(str(record[10].instances[8]), "GACCTGCCCCCCGCATAGTAG")
self.assertEqual(str(record[10].instances[9]), "AACCAGCGCATACCTTAACAG")
self.assertEqual(str(record[10].instances[10]), "ATCCTCTGCGTCGCATGGCGG")
self.assertEqual(str(record[10].instances[11]), "GACCATAGACGAGCATCAAAG")
self.assertEqual(str(record[10].instances[12]), "GGCCCTCGGATCGCTTGGGAA")
self.assertEqual(record[10].mask, (1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1))
self.assertAlmostEqual(record[10].score, 9.01393)
self.assertEqual(record[11].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[11].instances), 16)
self.assertEqual(str(record[11].instances[0]), "GCCGTCCGTC")
self.assertEqual(str(record[11].instances[1]), "GGCGTGCGCG")
self.assertEqual(str(record[11].instances[2]), "GGCGCGTGTC")
self.assertEqual(str(record[11].instances[3]), "AGCGCGTGTG")
self.assertEqual(str(record[11].instances[4]), "GCGGTGCGTG")
self.assertEqual(str(record[11].instances[5]), "AGCGCGTGTC")
self.assertEqual(str(record[11].instances[6]), "AGCGTCCGCG")
self.assertEqual(str(record[11].instances[7]), "ACCGTCTGTG")
self.assertEqual(str(record[11].instances[8]), "GCCATGCGAC")
self.assertEqual(str(record[11].instances[9]), "ACCACCCGTC")
self.assertEqual(str(record[11].instances[10]), "GGCGCCGGAG")
self.assertEqual(str(record[11].instances[11]), "ACCACGTGTC")
self.assertEqual(str(record[11].instances[12]), "GGCTTGCGAG")
self.assertEqual(str(record[11].instances[13]), "GCGATCCGAG")
self.assertEqual(str(record[11].instances[14]), "AGTGCGCGTC")
self.assertEqual(str(record[11].instances[15]), "AGTGCCCGAG")
self.assertEqual(record[11].mask, (1, 1, 1, 1, 1, 1, 1, 1, 1, 1))
self.assertAlmostEqual(record[11].score, 7.51121)
self.assertEqual(record[12].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[12].instances), 16)
self.assertEqual(str(record[12].instances[0]), "GCCGACGGGTGGTCATCGGG")
self.assertEqual(str(record[12].instances[1]), "GCACGACGCTTTGTACCTGG")
self.assertEqual(str(record[12].instances[2]), "CCTGGGAGGGTTCAATAACG")
self.assertEqual(str(record[12].instances[3]), "GCGCGTCCCGGGCCAATAGC")
self.assertEqual(str(record[12].instances[4]), "GCCGTCTGCTGGACAACGGG")
self.assertEqual(str(record[12].instances[5]), "GTCCCTTCCGGTACATGAGG")
self.assertEqual(str(record[12].instances[6]), "GCTGCTCCCCGCATACAGCG")
self.assertEqual(str(record[12].instances[7]), "GCCCCAAGCTTACCCAGGGA")
self.assertEqual(str(record[12].instances[8]), "ACCGGCTGACGCTAATACGG")
self.assertEqual(str(record[12].instances[9]), "GCGGGGGGCAGGTCATTACA")
self.assertEqual(str(record[12].instances[10]), "GCTGGCAGCGTCTAAGAAGG")
self.assertEqual(str(record[12].instances[11]), "GCAGGTGGTCGTGCAATACG")
self.assertEqual(str(record[12].instances[12]), "GCTGGTTGAAGTCCCGTGCG")
self.assertEqual(str(record[12].instances[13]), "GCACGTAGCTGGTAAATAGG")
self.assertEqual(str(record[12].instances[14]), "GCGGCGTGGATTTCATACAG")
self.assertEqual(str(record[12].instances[15]), "CCTGGAGGCTTAGACTTGGG")
self.assertEqual(record[12].mask, (1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1))
self.assertAlmostEqual(record[12].score, 5.63667)
self.assertEqual(record[13].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[13].instances), 15)
self.assertEqual(str(record[13].instances[0]), "GCCGACGGGTGGTCATCGGG")
self.assertEqual(str(record[13].instances[1]), "ATCCGCGGACGCTTAGAGGG")
self.assertEqual(str(record[13].instances[2]), "ACGCTTTGTACCTGGCTTGC")
self.assertEqual(str(record[13].instances[3]), "ACGGACGGCACTTAGCAGCG")
self.assertEqual(str(record[13].instances[4]), "GCCGTCTGCTGGACAACGGG")
self.assertEqual(str(record[13].instances[5]), "ACACACAGACGGTTGAAAGG")
self.assertEqual(str(record[13].instances[6]), "GCCGATAGTGCTTAAGTTCG")
self.assertEqual(str(record[13].instances[7]), "CTTGCCCGTACCGGACCTCG")
self.assertEqual(str(record[13].instances[8]), "ACCGGCTGACGCTAATACGG")
self.assertEqual(str(record[13].instances[9]), "GCCCCCCGCATAGTAGGGGG")
self.assertEqual(str(record[13].instances[10]), "GCTGGCAGCGTCTAAGAAGG")
self.assertEqual(str(record[13].instances[11]), "GCAGGTGGTCGTGCAATACG")
self.assertEqual(str(record[13].instances[12]), "ACGCACGGGACTTCAACCAG")
self.assertEqual(str(record[13].instances[13]), "GCACGTAGCTGGTAAATAGG")
self.assertEqual(str(record[13].instances[14]), "ATCCTCTGCGTCGCATGGCG")
self.assertEqual(record[13].mask, (1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1))
self.assertAlmostEqual(record[13].score, 3.89842)
self.assertEqual(record[14].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[14].instances), 14)
self.assertEqual(str(record[14].instances[0]), "GAGGCTGTGTAT")
self.assertEqual(str(record[14].instances[1]), "GAGGTCGGGGGT")
self.assertEqual(str(record[14].instances[2]), "GACGGACGGCAC")
self.assertEqual(str(record[14].instances[3]), "TTGGCCCGGGAC")
self.assertEqual(str(record[14].instances[4]), "GAGGCTCGGCCC")
self.assertEqual(str(record[14].instances[5]), "CACGCGCTGTAT")
self.assertEqual(str(record[14].instances[6]), "TAGGCCAGGTAT")
self.assertEqual(str(record[14].instances[7]), "GAGGTCCGGTAC")
self.assertEqual(str(record[14].instances[8]), "TACGCTGGGGAT")
self.assertEqual(str(record[14].instances[9]), "GTCGCGGAGGAT")
self.assertEqual(str(record[14].instances[10]), "TACGCACGGGAC")
self.assertEqual(str(record[14].instances[11]), "TACTCCGGGTAC")
self.assertEqual(str(record[14].instances[12]), "GACGCAGAGGAT")
self.assertEqual(str(record[14].instances[13]), "TAGGCGGGCCAT")
self.assertEqual(record[14].mask, (1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1))
self.assertAlmostEqual(record[14].score, 3.33444)
self.assertEqual(record[15].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record[15].instances), 21)
self.assertEqual(str(record[15].instances[0]), "CGGCTCAATCGTAGAGGC")
self.assertEqual(str(record[15].instances[1]), "CGACGGGTGGTCATCGGG")
self.assertEqual(str(record[15].instances[2]), "CGCTTAGAGGGCACAAGC")
self.assertEqual(str(record[15].instances[3]), "TGACACGCGCCTGGGAGG")
self.assertEqual(str(record[15].instances[4]), "CGATACGCTGCTAAGTGC")
self.assertEqual(str(record[15].instances[5]), "CGTCCCGGGCCAATAGCG")
self.assertEqual(str(record[15].instances[6]), "CCACGCTTCGACACGTGG")
self.assertEqual(str(record[15].instances[7]), "CGTCTGCTGGACAACGGG")
self.assertEqual(str(record[15].instances[8]), "ACACAGACGGTTGAAAGG")
self.assertEqual(str(record[15].instances[9]), "TGCTCCCCGCATACAGCG")
self.assertEqual(str(record[15].instances[10]), "TGAGGCTTGCCCGTACCG")
self.assertEqual(str(record[15].instances[11]), "TGCCCCAAGCTTACCCAG")
self.assertEqual(str(record[15].instances[12]), "CGGCTGACGCTAATACGG")
self.assertEqual(str(record[15].instances[13]), "CGCGACGTCCCTATGAGC")
self.assertEqual(str(record[15].instances[14]), "TGCCCCCCGCATAGTAGG")
self.assertEqual(str(record[15].instances[15]), "CGTTGCCTTCTTAGACGC")
self.assertEqual(str(record[15].instances[16]), "TGACTCAATCGTAGACCC")
self.assertEqual(str(record[15].instances[17]), "AGTCCCGTGCGTATGTGG")
self.assertEqual(str(record[15].instances[18]), "AGGCTCGCACGTAGCTGG")
self.assertEqual(str(record[15].instances[19]), "CCACGCCGCCATGCGACG")
self.assertEqual(str(record[15].instances[20]), "AGCCTCCAGGTCGCATGG")
self.assertEqual(record[15].mask, (1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0, 1, 1))
self.assertAlmostEqual(record[15].score, 1.0395)
def test_pfm_parsing(self):
"""Test if Bio.motifs can parse JASPAR-style pfm files.
"""
m = motifs.read(self.PFMin, "pfm")
self.assertEqual(m.length, 12)
def test_sites_parsing(self):
"""Test if Bio.motifs can parse JASPAR-style sites files.
"""
m = motifs.read(self.SITESin, "sites")
self.assertEqual(m.length, 6)
def test_TFoutput(self):
"""Ensure that we can write proper TransFac output files.
"""
output_handle = open(self.TFout, "w")
output_handle.write(self.m.format("transfac"))
output_handle.close()
def test_format(self):
self.m.name = 'Foo'
s1 = self.m.format('pfm')
expected_pfm = """ 1.00 0.00 1.00 0.00 1.00
0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00
0.00 1.00 0.00 1.00 0.00
"""
s2 = self.m.format('jaspar')
expected_jaspar = """>None Foo
A [ 1.00 0.00 1.00 0.00 1.00]
C [ 0.00 0.00 0.00 0.00 0.00]
G [ 0.00 0.00 0.00 0.00 0.00]
T [ 0.00 1.00 0.00 1.00 0.00]
"""
self.assertEqual(s2, expected_jaspar)
s3 = self.m.format('transfac')
expected_transfac = """P0 A C G T
01 1 0 0 0 A
02 0 0 0 1 T
03 1 0 0 0 A
04 0 0 0 1 T
05 1 0 0 0 A
XX
//
"""
self.assertEqual(s3, expected_transfac)
self.assertRaises(ValueError, self.m.format, 'foo_bar')
class TestMEME(unittest.TestCase):
def test_meme_parser_1(self):
"""Test if Bio.motifs can parse MEME output files (first test)
"""
handle = open("motifs/meme.out")
record = motifs.parse(handle, 'meme')
self.assertEqual(record.version, '3.5.7')
self.assertEqual(record.datafile, 'test.fa')
self.assertEqual(record.alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.sequences), 10)
self.assertEqual(record.sequences[0], 'SEQ1;')
self.assertEqual(record.sequences[1], 'SEQ2;')
self.assertEqual(record.sequences[2], 'SEQ3;')
self.assertEqual(record.sequences[3], 'SEQ4;')
self.assertEqual(record.sequences[4], 'SEQ5;')
self.assertEqual(record.sequences[5], 'SEQ6;')
self.assertEqual(record.sequences[6], 'SEQ7;')
self.assertEqual(record.sequences[7], 'SEQ8;')
self.assertEqual(record.sequences[8], 'SEQ9;')
self.assertEqual(record.sequences[9], 'SEQ10;')
self.assertEqual(record.command, 'meme test.fa -dna -w 10 -dir /home/bartek/MetaMotif/meme')
self.assertEqual(len(record), 1)
motif = record[0]
self.assertEqual(motif.name, "Motif 1")
self.assertEqual(record["Motif 1"], motif)
self.assertEqual(motif.num_occurrences, 10)
self.assertAlmostEqual(motif.evalue, 1.1e-22)
self.assertEqual(motif.alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(motif.instances), 10)
self.assertAlmostEqual(motif.instances[0].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[1].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[2].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[3].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[4].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[5].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[6].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[7].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[8].pvalue, 8.71e-07)
self.assertAlmostEqual(motif.instances[9].pvalue, 8.71e-07)
self.assertEqual(motif.instances[0].sequence_name, 'SEQ10;')
self.assertEqual(motif.instances[1].sequence_name, 'SEQ9;')
self.assertEqual(motif.instances[2].sequence_name, 'SEQ8;')
self.assertEqual(motif.instances[3].sequence_name, 'SEQ7;')
self.assertEqual(motif.instances[4].sequence_name, 'SEQ6;')
self.assertEqual(motif.instances[5].sequence_name, 'SEQ5;')
self.assertEqual(motif.instances[6].sequence_name, 'SEQ4;')
self.assertEqual(motif.instances[7].sequence_name, 'SEQ3;')
self.assertEqual(motif.instances[8].sequence_name, 'SEQ2;')
self.assertEqual(motif.instances[9].sequence_name, 'SEQ1;')
self.assertEqual(motif.instances[0].start, 3)
self.assertEqual(motif.instances[1].start, 93)
self.assertEqual(motif.instances[2].start, 172)
self.assertEqual(motif.instances[3].start, 177)
self.assertEqual(motif.instances[4].start, 105)
self.assertEqual(motif.instances[5].start, 185)
self.assertEqual(motif.instances[6].start, 173)
self.assertEqual(motif.instances[7].start, 112)
self.assertEqual(motif.instances[8].start, 172)
self.assertEqual(motif.instances[9].start, 52)
self.assertEqual(motif.instances[0].strand, '+')
self.assertEqual(motif.instances[1].strand, '+')
self.assertEqual(motif.instances[2].strand, '+')
self.assertEqual(motif.instances[3].strand, '+')
self.assertEqual(motif.instances[4].strand, '+')
self.assertEqual(motif.instances[5].strand, '+')
self.assertEqual(motif.instances[6].strand, '+')
self.assertEqual(motif.instances[7].strand, '+')
self.assertEqual(motif.instances[8].strand, '+')
self.assertEqual(motif.instances[9].strand, '+')
self.assertEqual(motif.instances[0].length, 10)
self.assertEqual(motif.instances[1].length, 10)
self.assertEqual(motif.instances[2].length, 10)
self.assertEqual(motif.instances[3].length, 10)
self.assertEqual(motif.instances[4].length, 10)
self.assertEqual(motif.instances[5].length, 10)
self.assertEqual(motif.instances[6].length, 10)
self.assertEqual(motif.instances[7].length, 10)
self.assertEqual(motif.instances[8].length, 10)
self.assertEqual(motif.instances[9].length, 10)
self.assertEqual(motif.instances[0].motif_name, 'Motif 1')
self.assertEqual(motif.instances[1].motif_name, 'Motif 1')
self.assertEqual(motif.instances[2].motif_name, 'Motif 1')
self.assertEqual(motif.instances[3].motif_name, 'Motif 1')
self.assertEqual(motif.instances[4].motif_name, 'Motif 1')
self.assertEqual(motif.instances[5].motif_name, 'Motif 1')
self.assertEqual(motif.instances[6].motif_name, 'Motif 1')
self.assertEqual(motif.instances[7].motif_name, 'Motif 1')
self.assertEqual(motif.instances[8].motif_name, 'Motif 1')
self.assertEqual(motif.instances[9].motif_name, 'Motif 1')
self.assertEqual(motif.instances[0].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[1].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[2].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[3].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[4].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[5].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[6].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[7].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[8].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(motif.instances[9].alphabet, IUPAC.unambiguous_dna)
self.assertEqual(str(motif.instances[0]), "CTCAATCGTA")
self.assertEqual(str(motif.instances[1]), "CTCAATCGTA")
self.assertEqual(str(motif.instances[2]), "CTCAATCGTA")
self.assertEqual(str(motif.instances[3]), "CTCAATCGTA")
self.assertEqual(str(motif.instances[4]), "CTCAATCGTA")
self.assertEqual(str(motif.instances[5]), "CTCAATCGTA")
self.assertEqual(str(motif.instances[6]), "CTCAATCGTA")
self.assertEqual(str(motif.instances[7]), "CTCAATCGTA")
self.assertEqual(str(motif.instances[8]), "CTCAATCGTA")
self.assertEqual(str(motif.instances[9]), "CTCAATCGTA")
handle.close()
def test_meme_parser_2(self):
"""Test if Bio.motifs can parse MEME output files (second test)
"""
handle = open("motifs/meme.dna.oops.txt")
record = motifs.parse(handle, 'meme')
self.assertEqual(record.version, '3.0')
self.assertEqual(record.datafile, 'INO_up800.s')
self.assertEqual(record.alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(record.sequences), 7)
self.assertEqual(record.sequences[0], 'CHO1')
self.assertEqual(record.sequences[1], 'CHO2')
self.assertEqual(record.sequences[2], 'FAS1')
self.assertEqual(record.sequences[3], 'FAS2')
self.assertEqual(record.sequences[4], 'ACC1')
self.assertEqual(record.sequences[5], 'INO1')
self.assertEqual(record.sequences[6], 'OPI3')
self.assertEqual(record.command, 'meme -mod oops -dna -revcomp -nmotifs 2 -bfile yeast.nc.6.freq INO_up800.s')
self.assertEqual(len(record), 2)
motif = record[0]
self.assertEqual(motif.name, "Motif 1")
self.assertEqual(record["Motif 1"], motif)
self.assertEqual(motif.num_occurrences, 7)
self.assertAlmostEqual(motif.evalue, 0.2)
self.assertEqual(motif.alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(motif.instances), 7)
self.assertAlmostEqual(motif.instances[0].pvalue, 1.85e-08)
self.assertAlmostEqual(motif.instances[1].pvalue, 1.85e-08)
self.assertAlmostEqual(motif.instances[2].pvalue, 1.52e-07)
self.assertAlmostEqual(motif.instances[3].pvalue, 2.52e-07)
self.assertAlmostEqual(motif.instances[4].pvalue, 4.23e-07)
self.assertAlmostEqual(motif.instances[5].pvalue, 9.43e-07)
self.assertAlmostEqual(motif.instances[6].pvalue, 3.32e-06)
self.assertEqual(motif.instances[0].sequence_name, 'INO1')
self.assertEqual(motif.instances[1].sequence_name, 'FAS1')
self.assertEqual(motif.instances[2].sequence_name, 'ACC1')
self.assertEqual(motif.instances[3].sequence_name, 'CHO2')
self.assertEqual(motif.instances[4].sequence_name, 'CHO1')
self.assertEqual(motif.instances[5].sequence_name, 'FAS2')
self.assertEqual(motif.instances[6].sequence_name, 'OPI3')
self.assertEqual(motif.instances[0].strand, '-')
self.assertEqual(motif.instances[1].strand, '+')
self.assertEqual(motif.instances[2].strand, '+')
self.assertEqual(motif.instances[3].strand, '+')
self.assertEqual(motif.instances[4].strand, '+')
self.assertEqual(motif.instances[5].strand, '+')
self.assertEqual(motif.instances[6].strand, '+')
self.assertEqual(motif.instances[0].length, 12)
self.assertEqual(motif.instances[1].length, 12)
self.assertEqual(motif.instances[2].length, 12)
self.assertEqual(motif.instances[3].length, 12)
self.assertEqual(motif.instances[4].length, 12)
self.assertEqual(motif.instances[5].length, 12)
self.assertEqual(motif.instances[6].length, 12)
self.assertEqual(motif.instances[0].start, 620)
self.assertEqual(motif.instances[1].start, 95)
self.assertEqual(motif.instances[2].start, 83)
self.assertEqual(motif.instances[3].start, 354)
self.assertEqual(motif.instances[4].start, 611)
self.assertEqual(motif.instances[5].start, 567)
self.assertEqual(motif.instances[6].start, 340)
self.assertEqual(str(motif.instances[0]), "TTCACATGCCGC")
self.assertEqual(str(motif.instances[1]), "TTCACATGCCGC")
self.assertEqual(str(motif.instances[2]), "TTCACATGGCCC")
self.assertEqual(str(motif.instances[3]), "TTCTCATGCCGC")
self.assertEqual(str(motif.instances[4]), "TTCACACGGCAC")
self.assertEqual(str(motif.instances[5]), "TTCACATGCTAC")
self.assertEqual(str(motif.instances[6]), "TTCAGATCGCTC")
motif = record[1]
self.assertEqual(motif.name, "Motif 2")
self.assertEqual(record["Motif 2"], motif)
self.assertEqual(motif.num_occurrences, 7)
self.assertAlmostEqual(motif.evalue, 110)
self.assertEqual(motif.alphabet, IUPAC.unambiguous_dna)
self.assertEqual(len(motif.instances), 7)
self.assertAlmostEqual(motif.instances[0].pvalue, 3.24e-07)
self.assertAlmostEqual(motif.instances[1].pvalue, 3.24e-07)
self.assertAlmostEqual(motif.instances[2].pvalue, 3.24e-07)
self.assertAlmostEqual(motif.instances[3].pvalue, 5.29e-06)
self.assertAlmostEqual(motif.instances[4].pvalue, 6.25e-06)
self.assertAlmostEqual(motif.instances[5].pvalue, 8.48e-06)
self.assertAlmostEqual(motif.instances[6].pvalue, 8.48e-06)
self.assertEqual(motif.instances[0].sequence_name, 'OPI3')
self.assertEqual(motif.instances[1].sequence_name, 'ACC1')
self.assertEqual(motif.instances[2].sequence_name, 'CHO1')
self.assertEqual(motif.instances[3].sequence_name, 'INO1')
self.assertEqual(motif.instances[4].sequence_name, 'FAS1')
self.assertEqual(motif.instances[5].sequence_name, 'FAS2')
self.assertEqual(motif.instances[6].sequence_name, 'CHO2')
self.assertEqual(motif.instances[0].strand, '-')
self.assertEqual(motif.instances[1].strand, '+')
self.assertEqual(motif.instances[2].strand, '-')
self.assertEqual(motif.instances[3].strand, '-')
self.assertEqual(motif.instances[4].strand, '+')
self.assertEqual(motif.instances[5].strand, '-')
self.assertEqual(motif.instances[6].strand, '-')
self.assertEqual(motif.instances[0].length, 10)
self.assertEqual(motif.instances[1].length, 10)
self.assertEqual(motif.instances[2].length, 10)
self.assertEqual(motif.instances[3].length, 10)
self.assertEqual(motif.instances[4].length, 10)
self.assertEqual(motif.instances[5].length, 10)
self.assertEqual(motif.instances[6].length, 10)
self.assertEqual(motif.instances[0].start, 186)
self.assertEqual(motif.instances[1].start, 232)
self.assertEqual(motif.instances[2].start, 559)
self.assertEqual(motif.instances[3].start, 283)
self.assertEqual(motif.instances[4].start, 44)
self.assertEqual(motif.instances[5].start, 185)
self.assertEqual(motif.instances[6].start, 413)
self.assertEqual(str(motif.instances[0]), "TCTGGCACAG")
self.assertEqual(str(motif.instances[1]), "TCTGGCACAG")
self.assertEqual(str(motif.instances[2]), "TCTGGCACAG")
self.assertEqual(str(motif.instances[3]), "GCGGGCGCAG")
self.assertEqual(str(motif.instances[4]), "GCAGGCACGG")
self.assertEqual(str(motif.instances[5]), "TCTGGCACTC")
self.assertEqual(str(motif.instances[6]), "TCTGGCATCG")
handle.close()
def test_meme_parser_3(self):
"""Test if Bio.motifs can parse MEME output files (third test)
"""
handle = open("motifs/meme.protein.oops.txt")
record = motifs.parse(handle, 'meme')
self.assertEqual(record.version, '3.0')
self.assertEqual(record.datafile, 'adh.s')
self.assertEqual(record.alphabet, IUPAC.protein)
self.assertEqual(len(record.sequences), 33)
self.assertEqual(record.sequences[0], "2BHD_STREX")
self.assertEqual(record.sequences[1], "3BHD_COMTE")
self.assertEqual(record.sequences[2], "ADH_DROME")
self.assertEqual(record.sequences[3], "AP27_MOUSE")
self.assertEqual(record.sequences[4], "BA72_EUBSP")
self.assertEqual(record.sequences[5], "BDH_HUMAN")
self.assertEqual(record.sequences[6], "BPHB_PSEPS")
self.assertEqual(record.sequences[7], "BUDC_KLETE")
self.assertEqual(record.sequences[8], "DHES_HUMAN")
self.assertEqual(record.sequences[9], "DHGB_BACME")
self.assertEqual(record.sequences[10], "DHII_HUMAN")
self.assertEqual(record.sequences[11], "DHMA_FLAS1")
self.assertEqual(record.sequences[12], "ENTA_ECOLI")
self.assertEqual(record.sequences[13], "FIXR_BRAJA")
self.assertEqual(record.sequences[14], "GUTD_ECOLI")
self.assertEqual(record.sequences[15], "HDE_CANTR")
self.assertEqual(record.sequences[16], "HDHA_ECOLI")
self.assertEqual(record.sequences[17], "LIGD_PSEPA")
self.assertEqual(record.sequences[18], "NODG_RHIME")
self.assertEqual(record.sequences[19], "RIDH_KLEAE")
self.assertEqual(record.sequences[20], "YINL_LISMO")
self.assertEqual(record.sequences[21], "YRTP_BACSU")
self.assertEqual(record.sequences[22], "CSGA_MYXXA")
self.assertEqual(record.sequences[23], "DHB2_HUMAN")
self.assertEqual(record.sequences[24], "DHB3_HUMAN")
self.assertEqual(record.sequences[25], "DHCA_HUMAN")
self.assertEqual(record.sequences[26], "FABI_ECOLI")
self.assertEqual(record.sequences[27], "FVT1_HUMAN")
self.assertEqual(record.sequences[28], "HMTR_LEIMA")
self.assertEqual(record.sequences[29], "MAS1_AGRRA")
self.assertEqual(record.sequences[30], "PCR_PEA")
self.assertEqual(record.sequences[31], "RFBB_NEIGO")
self.assertEqual(record.sequences[32], "YURA_MYXXA")
self.assertEqual(record.command, 'meme adh.s -mod oops -protein -nmotifs 2')
self.assertEqual(len(record), 2)
motif = record[0]
self.assertEqual(motif.name, "Motif 1")
self.assertEqual(record["Motif 1"], motif)
self.assertEqual(motif.num_occurrences, 33)
self.assertAlmostEqual(motif.evalue, 3.6e-165)
self.assertEqual(motif.alphabet, IUPAC.protein)
self.assertEqual(len(motif.instances), 33)
self.assertAlmostEqual(motif.instances[0].pvalue, 1.64e-22)
self.assertAlmostEqual(motif.instances[1].pvalue, 6.32e-22)
self.assertAlmostEqual(motif.instances[2].pvalue, 1.13e-21)
self.assertAlmostEqual(motif.instances[3].pvalue, 4.04e-21)
self.assertAlmostEqual(motif.instances[4].pvalue, 6.12e-21)
self.assertAlmostEqual(motif.instances[5].pvalue, 7.52e-20)
self.assertAlmostEqual(motif.instances[6].pvalue, 3.35e-19)
self.assertAlmostEqual(motif.instances[7].pvalue, 4.82e-19)
self.assertAlmostEqual(motif.instances[8].pvalue, 4.82e-19)
self.assertAlmostEqual(motif.instances[9].pvalue, 1.11e-18)
self.assertAlmostEqual(motif.instances[10].pvalue, 1.25e-18)
self.assertAlmostEqual(motif.instances[11].pvalue, 2.23e-18)
self.assertAlmostEqual(motif.instances[12].pvalue, 5.53e-18)
self.assertAlmostEqual(motif.instances[13].pvalue, 9.65e-18)
self.assertAlmostEqual(motif.instances[14].pvalue, 2.86e-17)
self.assertAlmostEqual(motif.instances[15].pvalue, 8.20e-17)
self.assertAlmostEqual(motif.instances[16].pvalue, 9.09e-17)
self.assertAlmostEqual(motif.instances[17].pvalue, 1.37e-16)
self.assertAlmostEqual(motif.instances[18].pvalue, 2.52e-16)
self.assertAlmostEqual(motif.instances[19].pvalue, 1.21e-15)
self.assertAlmostEqual(motif.instances[20].pvalue, 1.61e-15)
self.assertAlmostEqual(motif.instances[21].pvalue, 1.77e-15)
self.assertAlmostEqual(motif.instances[22].pvalue, 7.81e-15)
self.assertAlmostEqual(motif.instances[23].pvalue, 8.55e-15)
self.assertAlmostEqual(motif.instances[24].pvalue, 1.47e-14)
self.assertAlmostEqual(motif.instances[25].pvalue, 3.24e-14)
self.assertAlmostEqual(motif.instances[26].pvalue, 1.80e-12)
self.assertAlmostEqual(motif.instances[27].pvalue, 2.10e-12)
self.assertAlmostEqual(motif.instances[28].pvalue, 4.15e-12)
self.assertAlmostEqual(motif.instances[29].pvalue, 5.20e-12)
self.assertAlmostEqual(motif.instances[30].pvalue, 4.80e-10)
self.assertAlmostEqual(motif.instances[31].pvalue, 2.77e-08)
self.assertAlmostEqual(motif.instances[32].pvalue, 5.72e-08)
self.assertEqual(motif.instances[0].sequence_name, 'YRTP_BACSU')
self.assertEqual(motif.instances[1].sequence_name, 'AP27_MOUSE')
self.assertEqual(motif.instances[2].sequence_name, 'NODG_RHIME')
self.assertEqual(motif.instances[3].sequence_name, 'BUDC_KLETE')
self.assertEqual(motif.instances[4].sequence_name, 'FIXR_BRAJA')
self.assertEqual(motif.instances[5].sequence_name, 'DHGB_BACME')
self.assertEqual(motif.instances[6].sequence_name, 'HMTR_LEIMA')
self.assertEqual(motif.instances[7].sequence_name, 'YURA_MYXXA')
self.assertEqual(motif.instances[8].sequence_name, 'GUTD_ECOLI')
self.assertEqual(motif.instances[9].sequence_name, '2BHD_STREX')
self.assertEqual(motif.instances[10].sequence_name, 'HDHA_ECOLI')
self.assertEqual(motif.instances[11].sequence_name, 'DHB2_HUMAN')
self.assertEqual(motif.instances[12].sequence_name, 'DHMA_FLAS1')
self.assertEqual(motif.instances[13].sequence_name, 'HDE_CANTR')
self.assertEqual(motif.instances[14].sequence_name, 'FVT1_HUMAN')
self.assertEqual(motif.instances[15].sequence_name, 'BDH_HUMAN')
self.assertEqual(motif.instances[16].sequence_name, 'RIDH_KLEAE')
self.assertEqual(motif.instances[17].sequence_name, 'DHES_HUMAN')
self.assertEqual(motif.instances[18].sequence_name, 'BA72_EUBSP')
self.assertEqual(motif.instances[19].sequence_name, 'LIGD_PSEPA')
self.assertEqual(motif.instances[20].sequence_name, 'DHII_HUMAN')
self.assertEqual(motif.instances[21].sequence_name, 'ENTA_ECOLI')
self.assertEqual(motif.instances[22].sequence_name, '3BHD_COMTE')
self.assertEqual(motif.instances[23].sequence_name, 'DHB3_HUMAN')
self.assertEqual(motif.instances[24].sequence_name, 'RFBB_NEIGO')
self.assertEqual(motif.instances[25].sequence_name, 'YINL_LISMO')
self.assertEqual(motif.instances[26].sequence_name, 'BPHB_PSEPS')
self.assertEqual(motif.instances[27].sequence_name, 'CSGA_MYXXA')
self.assertEqual(motif.instances[28].sequence_name, 'FABI_ECOLI')
self.assertEqual(motif.instances[29].sequence_name, 'ADH_DROME')
self.assertEqual(motif.instances[30].sequence_name, 'DHCA_HUMAN')
self.assertEqual(motif.instances[31].sequence_name, 'PCR_PEA')
self.assertEqual(motif.instances[32].sequence_name, 'MAS1_AGRRA')
self.assertEqual(motif.instances[0].strand, '+')
self.assertEqual(motif.instances[1].strand, '+')
self.assertEqual(motif.instances[2].strand, '+')
self.assertEqual(motif.instances[3].strand, '+')
self.assertEqual(motif.instances[4].strand, '+')
self.assertEqual(motif.instances[5].strand, '+')
self.assertEqual(motif.instances[6].strand, '+')
self.assertEqual(motif.instances[7].strand, '+')
self.assertEqual(motif.instances[8].strand, '+')
self.assertEqual(motif.instances[9].strand, '+')
self.assertEqual(motif.instances[10].strand, '+')
self.assertEqual(motif.instances[11].strand, '+')
self.assertEqual(motif.instances[12].strand, '+')
self.assertEqual(motif.instances[13].strand, '+')
self.assertEqual(motif.instances[14].strand, '+')
self.assertEqual(motif.instances[15].strand, '+')
self.assertEqual(motif.instances[16].strand, '+')
self.assertEqual(motif.instances[17].strand, '+')
self.assertEqual(motif.instances[18].strand, '+')
self.assertEqual(motif.instances[19].strand, '+')
self.assertEqual(motif.instances[20].strand, '+')
self.assertEqual(motif.instances[21].strand, '+')
self.assertEqual(motif.instances[22].strand, '+')
self.assertEqual(motif.instances[23].strand, '+')
self.assertEqual(motif.instances[24].strand, '+')
self.assertEqual(motif.instances[25].strand, '+')
self.assertEqual(motif.instances[26].strand, '+')
self.assertEqual(motif.instances[27].strand, '+')
self.assertEqual(motif.instances[28].strand, '+')
self.assertEqual(motif.instances[29].strand, '+')
self.assertEqual(motif.instances[30].strand, '+')
self.assertEqual(motif.instances[31].strand, '+')
self.assertEqual(motif.instances[32].strand, '+')
self.assertEqual(motif.instances[0].length, 29)
self.assertEqual(motif.instances[1].length, 29)
self.assertEqual(motif.instances[2].length, 29)
self.assertEqual(motif.instances[3].length, 29)
self.assertEqual(motif.instances[4].length, 29)
self.assertEqual(motif.instances[5].length, 29)
self.assertEqual(motif.instances[6].length, 29)
self.assertEqual(motif.instances[7].length, 29)
self.assertEqual(motif.instances[8].length, 29)
self.assertEqual(motif.instances[9].length, 29)
self.assertEqual(motif.instances[10].length, 29)
self.assertEqual(motif.instances[11].length, 29)
self.assertEqual(motif.instances[12].length, 29)
self.assertEqual(motif.instances[13].length, 29)
self.assertEqual(motif.instances[14].length, 29)
self.assertEqual(motif.instances[15].length, 29)
self.assertEqual(motif.instances[16].length, 29)
self.assertEqual(motif.instances[17].length, 29)
self.assertEqual(motif.instances[18].length, 29)
self.assertEqual(motif.instances[19].length, 29)
self.assertEqual(motif.instances[20].length, 29)
self.assertEqual(motif.instances[21].length, 29)
self.assertEqual(motif.instances[22].length, 29)
self.assertEqual(motif.instances[23].length, 29)
self.assertEqual(motif.instances[24].length, 29)
self.assertEqual(motif.instances[25].length, 29)
self.assertEqual(motif.instances[26].length, 29)
self.assertEqual(motif.instances[27].length, 29)
self.assertEqual(motif.instances[28].length, 29)
self.assertEqual(motif.instances[29].length, 29)
self.assertEqual(motif.instances[30].length, 29)
self.assertEqual(motif.instances[31].length, 29)
self.assertEqual(motif.instances[32].length, 29)
self.assertEqual(motif.instances[0].start, 155)
self.assertEqual(motif.instances[1].start, 149)
self.assertEqual(motif.instances[2].start, 152)
self.assertEqual(motif.instances[3].start, 152)
self.assertEqual(motif.instances[4].start, 189)
self.assertEqual(motif.instances[5].start, 160)
self.assertEqual(motif.instances[6].start, 193)
self.assertEqual(motif.instances[7].start, 160)
self.assertEqual(motif.instances[8].start, 154)
self.assertEqual(motif.instances[9].start, 152)
self.assertEqual(motif.instances[10].start, 159)
self.assertEqual(motif.instances[11].start, 232)
self.assertEqual(motif.instances[12].start, 165)
self.assertEqual(motif.instances[13].start, 467)
self.assertEqual(motif.instances[14].start, 186)
self.assertEqual(motif.instances[15].start, 208)
self.assertEqual(motif.instances[16].start, 160)
self.assertEqual(motif.instances[17].start, 155)
self.assertEqual(motif.instances[18].start, 157)
self.assertEqual(motif.instances[19].start, 157)
self.assertEqual(motif.instances[20].start, 183)
self.assertEqual(motif.instances[21].start, 144)
self.assertEqual(motif.instances[22].start, 151)
self.assertEqual(motif.instances[23].start, 198)
self.assertEqual(motif.instances[24].start, 165)
self.assertEqual(motif.instances[25].start, 154)
self.assertEqual(motif.instances[26].start, 153)
self.assertEqual(motif.instances[27].start, 88)
self.assertEqual(motif.instances[28].start, 159)
self.assertEqual(motif.instances[29].start, 152)
self.assertEqual(motif.instances[30].start, 193)
self.assertEqual(motif.instances[31].start, 26)
self.assertEqual(motif.instances[32].start, 349)
self.assertEqual(str(motif.instances[0]), "YSASKFAVLGLTESLMQEVRKHNIRVSAL")
self.assertEqual(str(motif.instances[1]), "YSSTKGAMTMLTKAMAMELGPHKIRVNSV")
self.assertEqual(str(motif.instances[2]), "YCASKAGMIGFSKSLAQEIATRNITVNCV")
self.assertEqual(str(motif.instances[3]), "YSSSKFAVRGLTQTAARDLAPLGITVNGF")
self.assertEqual(str(motif.instances[4]), "YATSKAALASLTRELAHDYAPHGIRVNAI")
self.assertEqual(str(motif.instances[5]), "YAASKGGMKLMTETLALEYAPKGIRVNNI")
self.assertEqual(str(motif.instances[6]), "YTMAKGALEGLTRSAALELAPLQIRVNGV")
self.assertEqual(str(motif.instances[7]), "YSASKAFLSTFMESLRVDLRGTGVRVTCI")
self.assertEqual(str(motif.instances[8]), "YSAAKFGGVGLTQSLALDLAEYGITVHSL")
self.assertEqual(str(motif.instances[9]), "YGASKWGVRGLSKLAAVELGTDRIRVNSV")
self.assertEqual(str(motif.instances[10]), "YASSKAAASHLVRNMAFDLGEKNIRVNGI")
self.assertEqual(str(motif.instances[11]), "YGSSKAAVTMFSSVMRLELSKWGIKVASI")
self.assertEqual(str(motif.instances[12]), "YVAAKGGVAMLTRAMAVDLARHGILVNMI")
self.assertEqual(str(motif.instances[13]), "YSSSKAGILGLSKTMAIEGAKNNIKVNIV")
self.assertEqual(str(motif.instances[14]), "YSASKFAIRGLAEALQMEVKPYNVYITVA")
self.assertEqual(str(motif.instances[15]), "YCITKFGVEAFSDCLRYEMYPLGVKVSVV")
self.assertEqual(str(motif.instances[16]), "YTASKFAVQAFVHTTRRQVAQYGVRVGAV")
self.assertEqual(str(motif.instances[17]), "YCASKFALEGLCESLAVLLLPFGVHLSLI")
self.assertEqual(str(motif.instances[18]), "YPASKASVIGLTHGLGREIIRKNIRVVGV")
self.assertEqual(str(motif.instances[19]), "YSAAKAASINLMEGYRQGLEKYGIGVSVC")
self.assertEqual(str(motif.instances[20]), "YSASKFALDGFFSSIRKEYSVSRVNVSIT")
self.assertEqual(str(motif.instances[21]), "YGASKAALKSLALSVGLELAGSGVRCNVV")
self.assertEqual(str(motif.instances[22]), "YSASKAAVSALTRAAALSCRKQGYAIRVN")
self.assertEqual(str(motif.instances[23]), "YSASKAFVCAFSKALQEEYKAKEVIIQVL")
self.assertEqual(str(motif.instances[24]), "YSASKAAADHLVRAWQRTYRLPSIVSNCS")
self.assertEqual(str(motif.instances[25]), "YGATKWAVRDLMEVLRMESAQEGTNIRTA")
self.assertEqual(str(motif.instances[26]), "YTAAKQAIVGLVRELAFELAPYVRVNGVG")
self.assertEqual(str(motif.instances[27]), "YRMSKAALNMAVRSMSTDLRPEGFVTVLL")
self.assertEqual(str(motif.instances[28]), "MGLAKASLEANVRYMANAMGPEGVRVNAI")
self.assertEqual(str(motif.instances[29]), "YSGTKAAVVNFTSSLAKLAPITGVTAYTV")
self.assertEqual(str(motif.instances[30]), "YGVTKIGVTVLSRIHARKLSEQRKGDKIL")
self.assertEqual(str(motif.instances[31]), "KDSTLFGVSSLSDSLKGDFTSSALRCKEL")
self.assertEqual(str(motif.instances[32]), "YINCVAPLRMTELCLPHLYETGSGRIVNI")
motif = record[1]
self.assertEqual(motif.name, "Motif 2")
self.assertEqual(record["Motif 2"], motif)
self.assertEqual(motif.num_occurrences, 33)
self.assertAlmostEqual(motif.evalue, 2.3e-159)
self.assertEqual(motif.alphabet, IUPAC.protein)
self.assertEqual(len(motif.instances), 33)
self.assertAlmostEqual(motif.instances[0].pvalue, 2.44e-23)
self.assertAlmostEqual(motif.instances[1].pvalue, 5.50e-23)
self.assertAlmostEqual(motif.instances[2].pvalue, 5.38e-22)
self.assertAlmostEqual(motif.instances[3].pvalue, 5.65e-20)
self.assertAlmostEqual(motif.instances[4].pvalue, 1.17e-19)
self.assertAlmostEqual(motif.instances[5].pvalue, 1.17e-19)
self.assertAlmostEqual(motif.instances[6].pvalue, 4.74e-19)
self.assertAlmostEqual(motif.instances[7].pvalue, 9.31e-19)
self.assertAlmostEqual(motif.instances[8].pvalue, 2.50e-18)
self.assertAlmostEqual(motif.instances[9].pvalue, 3.45e-18)
self.assertAlmostEqual(motif.instances[10].pvalue, 5.86e-18)
self.assertAlmostEqual(motif.instances[11].pvalue, 9.86e-18)
self.assertAlmostEqual(motif.instances[12].pvalue, 2.47e-17)
self.assertAlmostEqual(motif.instances[13].pvalue, 3.01e-17)
self.assertAlmostEqual(motif.instances[14].pvalue, 3.33e-17)
self.assertAlmostEqual(motif.instances[15].pvalue, 4.06e-17)
self.assertAlmostEqual(motif.instances[16].pvalue, 4.06e-17)
self.assertAlmostEqual(motif.instances[17].pvalue, 8.05e-17)
self.assertAlmostEqual(motif.instances[18].pvalue, 1.90e-16)
self.assertAlmostEqual(motif.instances[19].pvalue, 2.77e-16)
self.assertAlmostEqual(motif.instances[20].pvalue, 3.65e-16)
self.assertAlmostEqual(motif.instances[21].pvalue, 8.31e-16)
self.assertAlmostEqual(motif.instances[22].pvalue, 4.05e-15)
self.assertAlmostEqual(motif.instances[23].pvalue, 5.24e-15)
self.assertAlmostEqual(motif.instances[24].pvalue, 3.00e-14)
self.assertAlmostEqual(motif.instances[25].pvalue, 8.47e-14)
self.assertAlmostEqual(motif.instances[26].pvalue, 1.46e-13)
self.assertAlmostEqual(motif.instances[27].pvalue, 1.46e-13)
self.assertAlmostEqual(motif.instances[28].pvalue, 1.59e-12)
self.assertAlmostEqual(motif.instances[29].pvalue, 6.97e-10)
self.assertAlmostEqual(motif.instances[30].pvalue, 3.15e-09)
self.assertAlmostEqual(motif.instances[31].pvalue, 2.77e-07)
self.assertAlmostEqual(motif.instances[32].pvalue, 4.24e-07)
self.assertEqual(motif.instances[0].sequence_name, 'HDE_CANTR')
self.assertEqual(motif.instances[1].sequence_name, 'DHII_HUMAN')
self.assertEqual(motif.instances[2].sequence_name, 'YINL_LISMO')
self.assertEqual(motif.instances[3].sequence_name, 'HDHA_ECOLI')
self.assertEqual(motif.instances[4].sequence_name, 'RIDH_KLEAE')
self.assertEqual(motif.instances[5].sequence_name, 'BUDC_KLETE')
self.assertEqual(motif.instances[6].sequence_name, 'ENTA_ECOLI')
self.assertEqual(motif.instances[7].sequence_name, 'AP27_MOUSE')
self.assertEqual(motif.instances[8].sequence_name, 'DHMA_FLAS1')
self.assertEqual(motif.instances[9].sequence_name, 'YRTP_BACSU')
self.assertEqual(motif.instances[10].sequence_name, 'DHGB_BACME')
self.assertEqual(motif.instances[11].sequence_name, 'DHB3_HUMAN')
self.assertEqual(motif.instances[12].sequence_name, 'PCR_PEA')
self.assertEqual(motif.instances[13].sequence_name, 'BDH_HUMAN')
self.assertEqual(motif.instances[14].sequence_name, 'BA72_EUBSP')
self.assertEqual(motif.instances[15].sequence_name, 'FIXR_BRAJA')
self.assertEqual(motif.instances[16].sequence_name, '3BHD_COMTE')
self.assertEqual(motif.instances[17].sequence_name, '2BHD_STREX')
self.assertEqual(motif.instances[18].sequence_name, 'HMTR_LEIMA')
self.assertEqual(motif.instances[19].sequence_name, 'FVT1_HUMAN')
self.assertEqual(motif.instances[20].sequence_name, 'DHB2_HUMAN')
self.assertEqual(motif.instances[21].sequence_name, 'LIGD_PSEPA')
self.assertEqual(motif.instances[22].sequence_name, 'NODG_RHIME')
self.assertEqual(motif.instances[23].sequence_name, 'DHCA_HUMAN')
self.assertEqual(motif.instances[24].sequence_name, 'MAS1_AGRRA')
self.assertEqual(motif.instances[25].sequence_name, 'BPHB_PSEPS')
self.assertEqual(motif.instances[26].sequence_name, 'GUTD_ECOLI')
self.assertEqual(motif.instances[27].sequence_name, 'DHES_HUMAN')
self.assertEqual(motif.instances[28].sequence_name, 'RFBB_NEIGO')
self.assertEqual(motif.instances[29].sequence_name, 'ADH_DROME')
self.assertEqual(motif.instances[30].sequence_name, 'FABI_ECOLI')
self.assertEqual(motif.instances[31].sequence_name, 'YURA_MYXXA')
self.assertEqual(motif.instances[32].sequence_name, 'CSGA_MYXXA')
self.assertEqual(motif.instances[0].start, 323)