forked from rrwick/Porechop
-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathadapters.py
628 lines (594 loc) · 31.9 KB
/
adapters.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
"""
Copyright 2017 Ryan Wick ([email protected])
https://github.com/rrwick/Porechop
This module contains the class and sequences for known adapters used in Oxford Nanopore library
preparation kits.
This file is part of Porechop. Porechop is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by the Free Software Foundation,
either version 3 of the License, or (at your option) any later version. Porechop is distributed in
the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details. You should have received a copy of the GNU General Public License along with Porechop. If
not, see <http://www.gnu.org/licenses/>.
"""
class Adapter(object):
def __init__(self, name, start_sequence=None, end_sequence=None, both_ends_sequence=None):
self.name = name
self.start_sequence = start_sequence if start_sequence else []
self.end_sequence = end_sequence if end_sequence else []
if both_ends_sequence:
self.start_sequence = both_ends_sequence
self.end_sequence = both_ends_sequence
self.best_start_score, self.best_end_score = 0.0, 0.0
def best_start_or_end_score(self):
return max(self.best_start_score, self.best_end_score)
def is_barcode(self):
return 'Barcode ' in self.name
def barcode_direction(self):
if '_rev' in self.start_sequence[0]:
return 'reverse'
else:
return 'forward'
def get_barcode_name(self):
"""
Gets the barcode name for the output files. We want a concise name, so it looks at all
options and chooses the shortest.
"""
possible_names = [self.name, self.start_sequence[0]]
if self.end_sequence:
possible_names.append(self.end_sequence[0])
barcode_name = sorted(possible_names, key=lambda x: len(x))[0]
return barcode_name.replace(' ', '_')
# INSTRUCTIONS FOR ADDING CUSTOM ADAPTERS
# ---------------------------------------
# If you need Porechop to remove adapters that aren't included, you can add your own my modifying
# the ADAPTERS list below.
#
# Here is the format for a normal adapter:
# Adapter('Adapter_set_name',
# start_sequence=('Start_adapter_name', 'AAAACCCCGGGGTTTTAAAACCCCGGGGTTTT'),
# end_sequence=('End_adapter_name', 'AACCGGTTAACCGGTTAACCGGTTAACCGGTT'))
#
# You can exclude start_sequence and end_sequence as appropriate.
#
# If you have custom Barcodes, make sure that the adapter set name starts with 'Barcode '. Also,
# remove the existing barcode sequences from this file to avoid conflicts:
# Adapter('Barcode 1',
# start_sequence=('Barcode_1_start', 'AAAAAAAACCCCCCCCGGGGGGGGTTTTTTTT'),
# end_sequence=('Barcode_1_end', 'AAAAAAAACCCCCCCCGGGGGGGGTTTTTTTT')),
# Adapter('Barcode 2',
# start_sequence=('Barcode_2_start', 'TTTTTTTTGGGGGGGGCCCCCCCCAAAAAAAA'),
# end_sequence=('Barcode_2_end', 'TTTTTTTTGGGGGGGGCCCCCCCCAAAAAAAA'))
NATIVE_BARCODES = [
# The native barcodes use the rev comp barcode at the start
# of the read and the forward barcode at the end of the read.
Adapter('Native Barcode 1',
start_sequence=('NB01_rev', 'CACAAAGACACCGACAACTTTCTT'),
end_sequence=('NB01', 'AAGAAAGTTGTCGGTGTCTTTGTG')),
Adapter('Native Barcode 2',
start_sequence=('NB02_rev', 'ACAGACGACTACAAACGGAATCGA'),
end_sequence=('NB02', 'TCGATTCCGTTTGTAGTCGTCTGT')),
Adapter('Native Barcode 3',
start_sequence=('NB03_rev', 'CCTGGTAACTGGGACACAAGACTC'),
end_sequence=('NB03', 'GAGTCTTGTGTCCCAGTTACCAGG')),
Adapter('Native Barcode 4',
start_sequence=('NB04_rev', 'TAGGGAAACACGATAGAATCCGAA'),
end_sequence=('NB04', 'TTCGGATTCTATCGTGTTTCCCTA')),
Adapter('Native Barcode 5',
start_sequence=('NB05_rev', 'AAGGTTACACAAACCCTGGACAAG'),
end_sequence=('NB05', 'CTTGTCCAGGGTTTGTGTAACCTT')),
Adapter('Native Barcode 6',
start_sequence=('NB06_rev', 'GACTACTTTCTGCCTTTGCGAGAA'),
end_sequence=('NB06', 'TTCTCGCAAAGGCAGAAAGTAGTC')),
Adapter('Native Barcode 7',
start_sequence=('NB07_rev', 'AAGGATTCATTCCCACGGTAACAC'),
end_sequence=('NB07', 'GTGTTACCGTGGGAATGAATCCTT')),
Adapter('Native Barcode 8',
start_sequence=('NB08_rev', 'ACGTAACTTGGTTTGTTCCCTGAA'),
end_sequence=('NB08', 'TTCAGGGAACAAACCAAGTTACGT')),
Adapter('Native Barcode 9',
start_sequence=('NB09_rev', 'AACCAAGACTCGCTGTGCCTAGTT'),
end_sequence=('NB09', 'AACTAGGCACAGCGAGTCTTGGTT')),
Adapter('Native Barcode 10',
start_sequence=('NB10_rev', 'GAGAGGACAAAGGTTTCAACGCTT'),
end_sequence=('NB10', 'AAGCGTTGAAACCTTTGTCCTCTC')),
Adapter('Native Barcode 11',
start_sequence=('NB11_rev', 'TCCATTCCCTCCGATAGATGAAAC'),
end_sequence=('NB11', 'GTTTCATCTATCGGAGGGAATGGA')),
Adapter('Native Barcode 12',
start_sequence=('NB12_rev', 'TCCGATTCTGCTTCTTTCTACCTG'),
end_sequence=('NB12', 'CAGGTAGAAAGAAGCAGAATCGGA')),
Adapter('Native Barcode 13',
start_sequence=('NB13_rev', 'AGAACGACTTCCATACTCGTGTGA'),
end_sequence=('NB13', 'TCACACGAGTATGGAAGTCGTTCT')),
Adapter('Native Barcode 14',
start_sequence=('NB14_rev', 'AACGAGTCTCTTGGGACCCATAGA'),
end_sequence=('NB14', 'TCTATGGGTCCCAAGAGACTCGTT')),
Adapter('Native Barcode 15',
start_sequence=('NB15_rev', 'AGGTCTACCTCGCTAACACCACTG'),
end_sequence=('NB15', 'CAGTGGTGTTAGCGAGGTAGACCT')),
Adapter('Native Barcode 16',
start_sequence=('NB16_rev', 'CGTCAACTGACAGTGGTTCGTACT'),
end_sequence=('NB16', 'AGTACGAACCACTGTCAGTTGACG')),
Adapter('Native Barcode 17',
start_sequence=('NB17_rev', 'ACCCTCCAGGAAAGTACCTCTGAT'),
end_sequence=('NB17', 'ATCAGAGGTACTTTCCTGGAGGGT')),
Adapter('Native Barcode 18',
start_sequence=('NB18_rev', 'CCAAACCCAACAACCTAGATAGGC'),
end_sequence=('NB18', 'GCCTATCTAGGTTGTTGGGTTTGG')),
Adapter('Native Barcode 19',
start_sequence=('NB19_rev', 'GTTCCTCGTGCAGTGTCAAGAGAT'),
end_sequence=('NB19', 'ATCTCTTGACACTGCACGAGGAAC')),
Adapter('Native Barcode 20',
start_sequence=('NB20_rev', 'TTGCGTCCTGTTACGAGAACTCAT'),
end_sequence=('NB20', 'ATGAGTTCTCGTAACAGGACGCAA')),
Adapter('Native Barcode 21',
start_sequence=('NB21_rev', 'GAGCCTCTCATTGTCCGTTCTCTA'),
end_sequence=('NB21', 'TAGAGAACGGACAATGAGAGGCTC')),
Adapter('Native Barcode 22',
start_sequence=('NB22_rev', 'ACCACTGCCATGTATCAAAGTACG'),
end_sequence=('NB22', 'CGTACTTTGATACATGGCAGTGGT')),
Adapter('Native Barcode 23',
start_sequence=('NB23_rev', 'CTTACTACCCAGTGAACCTCCTCG'),
end_sequence=('NB23', 'CGAGGAGGTTCACTGGGTAGTAAG')),
Adapter('Native Barcode 24',
start_sequence=('NB24_rev', 'GCATAGTTCTGCATGATGGGTTAG'),
end_sequence=('NB24', 'CTAACCCATCATGCAGAACTATGC'))]
PCR_BARCODES = [
# Other barcoding kits (like the PCR and rapid barcodes) use the forward barcode at the
# start of the read and the rev comp barcode at the end of the read.
Adapter('Barcode 1 (forward)',
start_sequence=('BC01', 'AAGAAAGTTGTCGGTGTCTTTGTG'),
end_sequence=('BC01_rev', 'CACAAAGACACCGACAACTTTCTT')),
Adapter('Barcode 2 (forward)',
start_sequence=('BC02', 'TCGATTCCGTTTGTAGTCGTCTGT'),
end_sequence=('BC02_rev', 'ACAGACGACTACAAACGGAATCGA')),
Adapter('Barcode 3 (forward)',
start_sequence=('BC03', 'GAGTCTTGTGTCCCAGTTACCAGG'),
end_sequence=('BC03_rev', 'CCTGGTAACTGGGACACAAGACTC')),
Adapter('Barcode 4 (forward)',
start_sequence=('BC04', 'TTCGGATTCTATCGTGTTTCCCTA'),
end_sequence=('BC04_rev', 'TAGGGAAACACGATAGAATCCGAA')),
Adapter('Barcode 5 (forward)',
start_sequence=('BC05', 'CTTGTCCAGGGTTTGTGTAACCTT'),
end_sequence=('BC05_rev', 'AAGGTTACACAAACCCTGGACAAG')),
Adapter('Barcode 6 (forward)',
start_sequence=('BC06', 'TTCTCGCAAAGGCAGAAAGTAGTC'),
end_sequence=('BC06_rev', 'GACTACTTTCTGCCTTTGCGAGAA')),
Adapter('Barcode 7 (forward)',
start_sequence=('BC07', 'GTGTTACCGTGGGAATGAATCCTT'),
end_sequence=('BC07_rev', 'AAGGATTCATTCCCACGGTAACAC')),
Adapter('Barcode 8 (forward)',
start_sequence=('BC08', 'TTCAGGGAACAAACCAAGTTACGT'),
end_sequence=('BC08_rev', 'ACGTAACTTGGTTTGTTCCCTGAA')),
Adapter('Barcode 9 (forward)',
start_sequence=('BC09', 'AACTAGGCACAGCGAGTCTTGGTT'),
end_sequence=('BC09_rev', 'AACCAAGACTCGCTGTGCCTAGTT')),
Adapter('Barcode 10 (forward)',
start_sequence=('BC10', 'AAGCGTTGAAACCTTTGTCCTCTC'),
end_sequence=('BC10_rev', 'GAGAGGACAAAGGTTTCAACGCTT')),
Adapter('Barcode 11 (forward)',
start_sequence=('BC11', 'GTTTCATCTATCGGAGGGAATGGA'),
end_sequence=('BC11_rev', 'TCCATTCCCTCCGATAGATGAAAC')),
Adapter('Barcode 12 (forward)',
start_sequence=('BC12', 'CAGGTAGAAAGAAGCAGAATCGGA'),
end_sequence=('BC12_rev', 'TCCGATTCTGCTTCTTTCTACCTG')),
Adapter('Barcode 13 (forward)',
start_sequence=('BC13', 'AGAACGACTTCCATACTCGTGTGA'),
end_sequence=('BC13_rev', 'TCACACGAGTATGGAAGTCGTTCT')),
Adapter('Barcode 14 (forward)',
start_sequence=('BC14', 'AACGAGTCTCTTGGGACCCATAGA'),
end_sequence=('BC14_rev', 'TCTATGGGTCCCAAGAGACTCGTT')),
Adapter('Barcode 15 (forward)',
start_sequence=('BC15', 'AGGTCTACCTCGCTAACACCACTG'),
end_sequence=('BC15_rev', 'CAGTGGTGTTAGCGAGGTAGACCT')),
Adapter('Barcode 16 (forward)',
start_sequence=('BC16', 'CGTCAACTGACAGTGGTTCGTACT'),
end_sequence=('BC16_rev', 'AGTACGAACCACTGTCAGTTGACG')),
Adapter('Barcode 17 (forward)',
start_sequence=('BC17', 'ACCCTCCAGGAAAGTACCTCTGAT'),
end_sequence=('BC17_rev', 'ATCAGAGGTACTTTCCTGGAGGGT')),
Adapter('Barcode 18 (forward)',
start_sequence=('BC18', 'CCAAACCCAACAACCTAGATAGGC'),
end_sequence=('BC18_rev', 'GCCTATCTAGGTTGTTGGGTTTGG')),
Adapter('Barcode 19 (forward)',
start_sequence=('BC19', 'GTTCCTCGTGCAGTGTCAAGAGAT'),
end_sequence=('BC19_rev', 'ATCTCTTGACACTGCACGAGGAAC')),
Adapter('Barcode 20 (forward)',
start_sequence=('BC20', 'TTGCGTCCTGTTACGAGAACTCAT'),
end_sequence=('BC20_rev', 'ATGAGTTCTCGTAACAGGACGCAA')),
Adapter('Barcode 21 (forward)',
start_sequence=('BC21', 'GAGCCTCTCATTGTCCGTTCTCTA'),
end_sequence=('BC21_rev', 'TAGAGAACGGACAATGAGAGGCTC')),
Adapter('Barcode 22 (forward)',
start_sequence=('BC22', 'ACCACTGCCATGTATCAAAGTACG'),
end_sequence=('BC22_rev', 'CGTACTTTGATACATGGCAGTGGT')),
Adapter('Barcode 23 (forward)',
start_sequence=('BC23', 'CTTACTACCCAGTGAACCTCCTCG'),
end_sequence=('BC23_rev', 'CGAGGAGGTTCACTGGGTAGTAAG')),
Adapter('Barcode 24 (forward)',
start_sequence=('BC24', 'GCATAGTTCTGCATGATGGGTTAG'),
end_sequence=('BC24_rev', 'CTAACCCATCATGCAGAACTATGC')),
Adapter('Barcode 25 (forward)',
start_sequence=('BC25', 'GTAAGTTGGGTATGCAACGCAATG'),
end_sequence=('BC25_rev', 'CATTGCGTTGCATACCCAACTTAC')),
Adapter('Barcode 26 (forward)',
start_sequence=('BC26', 'CATACAGCGACTACGCATTCTCAT'),
end_sequence=('BC26_rev', 'ATGAGAATGCGTAGTCGCTGTATG')),
Adapter('Barcode 27 (forward)',
start_sequence=('BC27', 'CGACGGTTAGATTCACCTCTTACA'),
end_sequence=('BC27_rev', 'TGTAAGAGGTGAATCTAACCGTCG')),
Adapter('Barcode 28 (forward)',
start_sequence=('BC28', 'TGAAACCTAAGAAGGCACCGTATC'),
end_sequence=('BC28_rev', 'GATACGGTGCCTTCTTAGGTTTCA')),
Adapter('Barcode 29 (forward)',
start_sequence=('BC29', 'CTAGACACCTTGGGTTGACAGACC'),
end_sequence=('BC29_rev', 'GGTCTGTCAACCCAAGGTGTCTAG')),
Adapter('Barcode 30 (forward)',
start_sequence=('BC30', 'TCAGTGAGGATCTACTTCGACCCA'),
end_sequence=('BC30_rev', 'TGGGTCGAAGTAGATCCTCACTGA')),
Adapter('Barcode 31 (forward)',
start_sequence=('BC31', 'TGCGTACAGCAATCAGTTACATTG'),
end_sequence=('BC31_rev', 'CAATGTAACTGATTGCTGTACGCA')),
Adapter('Barcode 32 (forward)',
start_sequence=('BC32', 'CCAGTAGAAGTCCGACAACGTCAT'),
end_sequence=('BC32_rev', 'ATGACGTTGTCGGACTTCTACTGG')),
Adapter('Barcode 33 (forward)',
start_sequence=('BC33', 'CAGACTTGGTACGGTTGGGTAACT'),
end_sequence=('BC33_rev', 'AGTTACCCAACCGTACCAAGTCTG')),
Adapter('Barcode 34 (forward)',
start_sequence=('BC34', 'GGACGAAGAACTCAAGTCAAAGGC'),
end_sequence=('BC34_rev', 'GCCTTTGACTTGAGTTCTTCGTCC')),
Adapter('Barcode 35 (forward)',
start_sequence=('BC35', 'CTACTTACGAAGCTGAGGGACTGC'),
end_sequence=('BC35_rev', 'GCAGTCCCTCAGCTTCGTAAGTAG')),
Adapter('Barcode 36 (forward)',
start_sequence=('BC36', 'ATGTCCCAGTTAGAGGAGGAAACA'),
end_sequence=('BC36_rev', 'TGTTTCCTCCTCTAACTGGGACAT')),
Adapter('Barcode 37 (forward)',
start_sequence=('BC37', 'GCTTGCGATTGATGCTTAGTATCA'),
end_sequence=('BC37_rev', 'TGATACTAAGCATCAATCGCAAGC')),
Adapter('Barcode 38 (forward)',
start_sequence=('BC38', 'ACCACAGGAGGACGATACAGAGAA'),
end_sequence=('BC38_rev', 'TTCTCTGTATCGTCCTCCTGTGGT')),
Adapter('Barcode 39 (forward)',
start_sequence=('BC39', 'CCACAGTGTCAACTAGAGCCTCTC'),
end_sequence=('BC39_rev', 'GAGAGGCTCTAGTTGACACTGTGG')),
Adapter('Barcode 40 (forward)',
start_sequence=('BC40', 'TAGTTTGGATGACCAAGGATAGCC'),
end_sequence=('BC40_rev', 'GGCTATCCTTGGTCATCCAAACTA')),
Adapter('Barcode 41 (forward)',
start_sequence=('BC41', 'GGAGTTCGTCCAGAGAAGTACACG'),
end_sequence=('BC41_rev', 'CGTGTACTTCTCTGGACGAACTCC')),
Adapter('Barcode 42 (forward)',
start_sequence=('BC42', 'CTACGTGTAAGGCATACCTGCCAG'),
end_sequence=('BC42_rev', 'CTGGCAGGTATGCCTTACACGTAG')),
Adapter('Barcode 43 (forward)',
start_sequence=('BC43', 'CTTTCGTTGTTGACTCGACGGTAG'),
end_sequence=('BC43_rev', 'CTACCGTCGAGTCAACAACGAAAG')),
Adapter('Barcode 44 (forward)',
start_sequence=('BC44', 'AGTAGAAAGGGTTCCTTCCCACTC'),
end_sequence=('BC44_rev', 'GAGTGGGAAGGAACCCTTTCTACT')),
Adapter('Barcode 45 (forward)',
start_sequence=('BC45', 'GATCCAACAGAGATGCCTTCAGTG'),
end_sequence=('BC45_rev', 'CACTGAAGGCATCTCTGTTGGATC')),
Adapter('Barcode 46 (forward)',
start_sequence=('BC46', 'GCTGTGTTCCACTTCATTCTCCTG'),
end_sequence=('BC46_rev', 'CAGGAGAATGAAGTGGAACACAGC')),
Adapter('Barcode 47 (forward)',
start_sequence=('BC47', 'GTGCAACTTTCCCACAGGTAGTTC'),
end_sequence=('BC47_rev', 'GAACTACCTGTGGGAAAGTTGCAC')),
Adapter('Barcode 48 (forward)',
start_sequence=('BC48', 'CATCTGGAACGTGGTACACCTGTA'),
end_sequence=('BC48_rev', 'TACAGGTGTACCACGTTCCAGATG')),
Adapter('Barcode 49 (forward)',
start_sequence=('BC49', 'ACTGGTGCAGCTTTGAACATCTAG'),
end_sequence=('BC49_rev', 'CTAGATGTTCAAAGCTGCACCAGT')),
Adapter('Barcode 50 (forward)',
start_sequence=('BC50', 'ATGGACTTTGGTAACTTCCTGCGT'),
end_sequence=('BC50_rev', 'ACGCAGGAAGTTACCAAAGTCCAT')),
Adapter('Barcode 51 (forward)',
start_sequence=('BC51', 'GTTGAATGAGCCTACTGGGTCCTC'),
end_sequence=('BC51_rev', 'GAGGACCCAGTAGGCTCATTCAAC')),
Adapter('Barcode 52 (forward)',
start_sequence=('BC52', 'TGAGAGACAAGATTGTTCGTGGAC'),
end_sequence=('BC52_rev', 'GTCCACGAACAATCTTGTCTCTCA')),
Adapter('Barcode 53 (forward)',
start_sequence=('BC53', 'AGATTCAGACCGTCTCATGCAAAG'),
end_sequence=('BC53_rev', 'CTTTGCATGAGACGGTCTGAATCT')),
Adapter('Barcode 54 (forward)',
start_sequence=('BC54', 'CAAGAGCTTTGACTAAGGAGCATG'),
end_sequence=('BC54_rev', 'CATGCTCCTTAGTCAAAGCTCTTG')),
Adapter('Barcode 55 (forward)',
start_sequence=('BC55', 'TGGAAGATGAGACCCTGATCTACG'),
end_sequence=('BC55_rev', 'CGTAGATCAGGGTCTCATCTTCCA')),
Adapter('Barcode 56 (forward)',
start_sequence=('BC56', 'TCACTACTCAACAGGTGGCATGAA'),
end_sequence=('BC56_rev', 'TTCATGCCACCTGTTGAGTAGTGA')),
Adapter('Barcode 57 (forward)',
start_sequence=('BC57', 'GCTAGGTCAATCTCCTTCGGAAGT'),
end_sequence=('BC57_rev', 'ACTTCCGAAGGAGATTGACCTAGC')),
Adapter('Barcode 58 (forward)',
start_sequence=('BC58', 'CAGGTTACTCCTCCGTGAGTCTGA'),
end_sequence=('BC58_rev', 'TCAGACTCACGGAGGAGTAACCTG')),
Adapter('Barcode 59 (forward)',
start_sequence=('BC59', 'TCAATCAAGAAGGGAAAGCAAGGT'),
end_sequence=('BC59_rev', 'ACCTTGCTTTCCCTTCTTGATTGA')),
Adapter('Barcode 60 (forward)',
start_sequence=('BC60', 'CATGTTCAACCAAGGCTTCTATGG'),
end_sequence=('BC60_rev', 'CCATAGAAGCCTTGGTTGAACATG')),
Adapter('Barcode 61 (forward)',
start_sequence=('BC61', 'AGAGGGTACTATGTGCCTCAGCAC'),
end_sequence=('BC61_rev', 'GTGCTGAGGCACATAGTACCCTCT')),
Adapter('Barcode 62 (forward)',
start_sequence=('BC62', 'CACCCACACTTACTTCAGGACGTA'),
end_sequence=('BC62_rev', 'TACGTCCTGAAGTAAGTGTGGGTG')),
Adapter('Barcode 63 (forward)',
start_sequence=('BC63', 'TTCTGAAGTTCCTGGGTCTTGAAC'),
end_sequence=('BC63_rev', 'GTTCAAGACCCAGGAACTTCAGAA')),
Adapter('Barcode 64 (forward)',
start_sequence=('BC64', 'GACAGACACCGTTCATCGACTTTC'),
end_sequence=('BC64_rev', 'GAAAGTCGATGAACGGTGTCTGTC')),
Adapter('Barcode 65 (forward)',
start_sequence=('BC65', 'TTCTCAGTCTTCCTCCAGACAAGG'),
end_sequence=('BC65_rev', 'CCTTGTCTGGAGGAAGACTGAGAA')),
Adapter('Barcode 66 (forward)',
start_sequence=('BC66', 'CCGATCCTTGTGGCTTCTAACTTC'),
end_sequence=('BC66_rev', 'GAAGTTAGAAGCCACAAGGATCGG')),
Adapter('Barcode 67 (forward)',
start_sequence=('BC67', 'GTTTGTCATACTCGTGTGCTCACC'),
end_sequence=('BC67_rev', 'GGTGAGCACACGAGTATGACAAAC')),
Adapter('Barcode 68 (forward)',
start_sequence=('BC68', 'GAATCTAAGCAAACACGAAGGTGG'),
end_sequence=('BC68_rev', 'CCACCTTCGTGTTTGCTTAGATTC')),
Adapter('Barcode 69 (forward)',
start_sequence=('BC69', 'TACAGTCCGAGCCTCATGTGATCT'),
end_sequence=('BC69_rev', 'AGATCACATGAGGCTCGGACTGTA')),
Adapter('Barcode 70 (forward)',
start_sequence=('BC70', 'ACCGAGATCCTACGAATGGAGTGT'),
end_sequence=('BC70_rev', 'ACACTCCATTCGTAGGATCTCGGT')),
Adapter('Barcode 71 (forward)',
start_sequence=('BC71', 'CCTGGGAGCATCAGGTAGTAACAG'),
end_sequence=('BC71_rev', 'CTGTTACTACCTGATGCTCCCAGG')),
Adapter('Barcode 72 (forward)',
start_sequence=('BC72', 'TAGCTGACTGTCTTCCATACCGAC'),
end_sequence=('BC72_rev', 'GTCGGTATGGAAGACAGTCAGCTA')),
Adapter('Barcode 73 (forward)',
start_sequence=('BC73', 'AAGAAACAGGATGACAGAACCCTC'),
end_sequence=('BC73_rev', 'GAGGGTTCTGTCATCCTGTTTCTT')),
Adapter('Barcode 74 (forward)',
start_sequence=('BC74', 'TACAAGCATCCCAACACTTCCACT'),
end_sequence=('BC74_rev', 'AGTGGAAGTGTTGGGATGCTTGTA')),
Adapter('Barcode 75 (forward)',
start_sequence=('BC75', 'GACCATTGTGATGAACCCTGTTGT'),
end_sequence=('BC75_rev', 'ACAACAGGGTTCATCACAATGGTC')),
Adapter('Barcode 76 (forward)',
start_sequence=('BC76', 'ATGCTTGTTACATCAACCCTGGAC'),
end_sequence=('BC76_rev', 'GTCCAGGGTTGATGTAACAAGCAT')),
Adapter('Barcode 77 (forward)',
start_sequence=('BC77', 'CGACCTGTTTCTCAGGGATACAAC'),
end_sequence=('BC77_rev', 'GTTGTATCCCTGAGAAACAGGTCG')),
Adapter('Barcode 78 (forward)',
start_sequence=('BC78', 'AACAACCGAACCTTTGAATCAGAA'),
end_sequence=('BC78_rev', 'TTCTGATTCAAAGGTTCGGTTGTT')),
Adapter('Barcode 79 (forward)',
start_sequence=('BC79', 'TCTCGGAGATAGTTCTCACTGCTG'),
end_sequence=('BC79_rev', 'CAGCAGTGAGAACTATCTCCGAGA')),
Adapter('Barcode 80 (forward)',
start_sequence=('BC80', 'CGGATGAACATAGGATAGCGATTC'),
end_sequence=('BC80_rev', 'GAATCGCTATCCTATGTTCATCCG')),
Adapter('Barcode 81 (forward)',
start_sequence=('BC81', 'CCTCATCTTGTGAAGTTGTTTCGG'),
end_sequence=('BC81_rev', 'CCGAAACAACTTCACAAGATGAGG')),
Adapter('Barcode 82 (forward)',
start_sequence=('BC82', 'ACGGTATGTCGAGTTCCAGGACTA'),
end_sequence=('BC82_rev', 'TAGTCCTGGAACTCGACATACCGT')),
Adapter('Barcode 83 (forward)',
start_sequence=('BC83', 'TGGCTTGATCTAGGTAAGGTCGAA'),
end_sequence=('BC83_rev', 'TTCGACCTTACCTAGATCAAGCCA')),
Adapter('Barcode 84 (forward)',
start_sequence=('BC84', 'GTAGTGGACCTAGAACCTGTGCCA'),
end_sequence=('BC84_rev', 'TGGCACAGGTTCTAGGTCCACTAC')),
Adapter('Barcode 85 (forward)',
start_sequence=('BC85', 'AACGGAGGAGTTAGTTGGATGATC'),
end_sequence=('BC85_rev', 'GATCATCCAACTAACTCCTCCGTT')),
Adapter('Barcode 86 (forward)',
start_sequence=('BC86', 'AGGTGATCCCAACAAGCGTAAGTA'),
end_sequence=('BC86_rev', 'TACTTACGCTTGTTGGGATCACCT')),
Adapter('Barcode 87 (forward)',
start_sequence=('BC87', 'TACATGCTCCTGTTGTTAGGGAGG'),
end_sequence=('BC87_rev', 'CCTCCCTAACAACAGGAGCATGTA')),
Adapter('Barcode 88 (forward)',
start_sequence=('BC88', 'TCTTCTACTACCGATCCGAAGCAG'),
end_sequence=('BC88_rev', 'CTGCTTCGGATCGGTAGTAGAAGA')),
Adapter('Barcode 89 (forward)',
start_sequence=('BC89', 'ACAGCATCAATGTTTGGCTAGTTG'),
end_sequence=('BC89_rev', 'CAACTAGCCAAACATTGATGCTGT')),
Adapter('Barcode 90 (forward)',
start_sequence=('BC90', 'GATGTAGAGGGTACGGTTTGAGGC'),
end_sequence=('BC90_rev', 'GCCTCAAACCGTACCCTCTACATC')),
Adapter('Barcode 91 (forward)',
start_sequence=('BC91', 'GGCTCCATAGGAACTCACGCTACT'),
end_sequence=('BC91_rev', 'AGTAGCGTGAGTTCCTATGGAGCC')),
Adapter('Barcode 92 (forward)',
start_sequence=('BC92', 'TTGTGAGTGGAAAGATACAGGACC'),
end_sequence=('BC92_rev', 'GGTCCTGTATCTTTCCACTCACAA')),
Adapter('Barcode 93 (forward)',
start_sequence=('BC93', 'AGTTTCCATCACTTCAGACTTGGG'),
end_sequence=('BC93_rev', 'CCCAAGTCTGAAGTGATGGAAACT')),
Adapter('Barcode 94 (forward)',
start_sequence=('BC94', 'GATTGTCCTCAAACTGCCACCTAC'),
end_sequence=('BC94_rev', 'GTAGGTGGCAGTTTGAGGACAATC')),
Adapter('Barcode 95 (forward)',
start_sequence=('BC95', 'CCTGTCTGGAAGAAGAATGGACTT'),
end_sequence=('BC95_rev', 'AAGTCCATTCTTCTTCCAGACAGG')),
Adapter('Barcode 96 (forward)',
start_sequence=('BC96', 'CTGAACGGTCATAGAGTCCACCAT'),
end_sequence=('BC96_rev', 'ATGGTGGACTCTATGACCGTTCAG'))]
RAPID_BARCODES = [
Adapter('Rapid Barcode 1 (reverse)',
start_sequence=('BC01', 'AAGAAAGTTGTCGGTGTCTTTGTG')),
Adapter('Rapid Barcode 2 (reverse)',
start_sequence=('BC02', 'TCGATTCCGTTTGTAGTCGTCTGT')),
Adapter('Rapid Barcode 3 (reverse)',
start_sequence=('BC03', 'GAGTCTTGTGTCCCAGTTACCAGG')),
Adapter('Rapid Barcode 4 (reverse)',
start_sequence=('BC04', 'TTCGGATTCTATCGTGTTTCCCTA')),
Adapter('Rapid Barcode 5 (reverse)',
start_sequence=('BC05', 'CTTGTCCAGGGTTTGTGTAACCTT')),
Adapter('Rapid Barcode 6 (reverse)',
start_sequence=('BC06', 'TTCTCGCAAAGGCAGAAAGTAGTC')),
Adapter('Rapid Barcode 7 (reverse)',
start_sequence=('BC07', 'GTGTTACCGTGGGAATGAATCCTT')),
Adapter('Rapid Barcode 8 (reverse)',
start_sequence=('BC08', 'TTCAGGGAACAAACCAAGTTACGT')),
Adapter('Rapid Barcode 9 (reverse)',
start_sequence=('BC09', 'AACTAGGCACAGCGAGTCTTGGTT')),
Adapter('Rapid Barcode 10 (reverse)',
start_sequence=('BC10', 'AAGCGTTGAAACCTTTGTCCTCTC')),
Adapter('Rapid Barcode 11 (reverse)',
start_sequence=('BC11', 'GTTTCATCTATCGGAGGGAATGGA')),
Adapter('Rapid Barcode 12 (reverse)',
start_sequence=('BC12', 'CAGGTAGAAAGAAGCAGAATCGGA')),
]
OTHER_ADAPTERS = [
Adapter('Barcode 13 (reverse)',
start_sequence=('BC13', 'AGAACGACTTCCATACTCGTGTGA'),
end_sequence=('BC13_rev', 'TCACACGAGTATGGAAGTCGTTCT')),
Adapter('Barcode 14 (reverse)',
start_sequence=('BC14', 'AACGAGTCTCTTGGGACCCATAGA'),
end_sequence=('BC14_rev', 'TCTATGGGTCCCAAGAGACTCGTT')),
Adapter('Barcode 15 (reverse)',
start_sequence=('BC15', 'AGGTCTACCTCGCTAACACCACTG'),
end_sequence=('BC15_rev', 'CAGTGGTGTTAGCGAGGTAGACCT')),
Adapter('Barcode 16 (reverse)',
start_sequence=('BC16', 'CGTCAACTGACAGTGGTTCGTACT'),
end_sequence=('BC16_rev', 'AGTACGAACCACTGTCAGTTGACG')),
Adapter('Barcode 17 (reverse)',
start_sequence=('BC17', 'ACCCTCCAGGAAAGTACCTCTGAT'),
end_sequence=('BC17_rev', 'ATCAGAGGTACTTTCCTGGAGGGT')),
Adapter('Barcode 18 (reverse)',
start_sequence=('BC18', 'CCAAACCCAACAACCTAGATAGGC'),
end_sequence=('BC18_rev', 'GCCTATCTAGGTTGTTGGGTTTGG')),
Adapter('Barcode 19 (reverse)',
start_sequence=('BC19', 'GTTCCTCGTGCAGTGTCAAGAGAT'),
end_sequence=('BC19_rev', 'ATCTCTTGACACTGCACGAGGAAC')),
Adapter('Barcode 20 (reverse)',
start_sequence=('BC20', 'TTGCGTCCTGTTACGAGAACTCAT'),
end_sequence=('BC20_rev', 'ATGAGTTCTCGTAACAGGACGCAA')),
Adapter('Barcode 21 (reverse)',
start_sequence=('BC21', 'GAGCCTCTCATTGTCCGTTCTCTA'),
end_sequence=('BC21_rev', 'TAGAGAACGGACAATGAGAGGCTC')),
Adapter('Barcode 22 (reverse)',
start_sequence=('BC22', 'ACCACTGCCATGTATCAAAGTACG'),
end_sequence=('BC22_rev', 'CGTACTTTGATACATGGCAGTGGT')),
Adapter('Barcode 23 (reverse)',
start_sequence=('BC23', 'CTTACTACCCAGTGAACCTCCTCG'),
end_sequence=('BC23_rev', 'CGAGGAGGTTCACTGGGTAGTAAG')),
Adapter('Barcode 24 (reverse)',
start_sequence=('BC24', 'GCATAGTTCTGCATGATGGGTTAG'),
end_sequence=('BC24_rev', 'CTAACCCATCATGCAGAACTATGC')),
Adapter('SQK-NSK007',
start_sequence=('SQK-NSK007_Y_Top', 'AATGTACTTCGTTCAGTTACGTATTGCT'),
end_sequence=('SQK-NSK007_Y_Bottom', 'GCAATACGTAACTGAACGAAGT')),
Adapter('Rapid',
start_sequence=('Rapid_adapter', 'GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA')),
Adapter('SQK-MAP006',
start_sequence=('SQK-MAP006_Y_Top_SK63', 'GGTTGTTTCTGTTGGTGCTGATATTGCT'),
end_sequence= ('SQK-MAP006_Y_Bottom_SK64', 'GCAATATCAGCACCAACAGAAA')),
Adapter('SQK-MAP006 Short',
start_sequence=('SQK-MAP006_Short_Y_Top_LI32', 'CGGCGTCTGCTTGGGTGTTTAACCT'),
end_sequence= ('SQK-MAP006_Short_Y_Bottom_LI33', 'GGTTAAACACCCAAGCAGACGCCG')),
Adapter('PCR adapters 1',
start_sequence=('PCR_1_start', 'ACTTGCCTGTCGCTCTATCTTC'),
end_sequence= ('PCR_1_end', 'GAAGATAGAGCGACAGGCAAGT')),
Adapter('PCR tail 1',
start_sequence=('PCR_tail_1_start', 'TTAACCTTTCTGTTGGTGCTGATATTGC'),
end_sequence= ('PCR_tail_1_end', 'GCAATATCAGCACCAACAGAAAGGTTAA')),
Adapter('PCR tail 2',
start_sequence=('PCR_tail_2_start', 'TTAACCTACTTGCCTGTCGCTCTATCTTC'),
end_sequence= ('PCR_tail_2_end', 'GAAGATAGAGCGACAGGCAAGTAGGTTAA')),
# 1D^2 kit adapters are interesting. ONT provided the following sequences on their site:
# start: GGCGTCTGCTTGGGTGTTTAACCTTTTTGTCAGAGAGGTTCCAAGTCAGAGAGGTTCCT
# end: GGAACCTCTCTCTGACTTGGAACCTCTCTGACAAAAAGGTTAAACACCCAAGCAGACGCCAGCAAT
# But when looking at actual reads, I found two parts. The first corresponds to one end
# of the provided sequences (through slightly different):
Adapter('1D^2 part 1',
start_sequence=('1D2_part_1_start', 'GAGAGGTTCCAAGTCAGAGAGGTTCCT'),
end_sequence= ('1D2_part_1_end', 'AGGAACCTCTCTGACTTGGAACCTCTC')),
# and the second part corresponds to the other end, combined with a bit of standard 1D
# adapter:
Adapter('1D^2 part 2',
start_sequence=('1D2_part_2_start', 'CTTCGTTCAGTTACGTATTGCTGGCGTCTGCTT'),
end_sequence= ('1D2_part_2_end', 'CACCCAAGCAGACGCCAGCAATACGTAACT')),
# The middle part of the provided sequences is less common, so I've left it out of the
# adapter sequences here.
]
def make_full_native_barcode_adapter(barcode_num):
barcode = [x for x in NATIVE_BARCODES if x.name == 'Native Barcode ' + str(barcode_num)][0]
start_barcode_seq = barcode.start_sequence[1]
end_barcode_seq = barcode.end_sequence[1]
start_full_seq = 'AATGTACTTCGTTCAGTTACGTATTGCTAAGGTTAA' + start_barcode_seq + 'CAGCACCT'
end_full_seq = 'AGGTGCTG' + end_barcode_seq + 'TTAACCTTAGCAATACGTAACTGAACGAAGT'
return Adapter('Native barcoding ' + str(barcode_num) + ' (full sequence)',
start_sequence=('NB' + '%02d' % barcode_num + '_start', start_full_seq),
end_sequence=('NB' + '%02d' % barcode_num + '_end', end_full_seq))
def make_full_rapid_barcode_adapter(barcode_num):
barcode = [x for x in ALL_ADAPTERS if x.name == 'Barcode ' + str(barcode_num) + ' (forward)'][0]
start_barcode_seq = barcode.start_sequence[1]
start_full_seq = 'AATGTACTTCGTTCAGTTACGTATTGCT' + start_barcode_seq + 'GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA'
return Adapter('Rapid barcoding ' + str(barcode_num) + ' (full sequence)',
start_sequence=('RB' + '%02d' % barcode_num + '_full', start_full_seq))
def load_primers(primer_file):
c = 0
# file should be csv eg:
# primer1_LEFT,seq\n
# primer1_right,seq\n
# primer2_LEFT,seq\n
# primer2_right,seq\n
print("Loading primers from file {}...".format(primer_file))
CUSTOM_BARCODES=[]
start_name=''
end_name=''
name=''
custom_barcodes = str(primer_file)
with open(custom_barcodes,"r") as f:
for l in f:
c +=1
tokens=l.split(',')
if c%2!=0:
name='Barcode {} (forward)'.format(tokens[0].rstrip('_LEFT'))
start_name=tokens[0]
start_seq=tokens[1]
else:
if name=='Barcode {} (forward)'.format(tokens[0].rstrip('_RIGHT')):
end_name=tokens[0]
end_seq=tokens[1]
print(name, start_name, end_name, start_seq, end_seq)
CUSTOM_BARCODES.append(Adapter(name, start_sequence=(start_name, start_seq), end_sequence=(end_name, end_seq)))
return CUSTOM_BARCODES
def load_custom_barcodes(custom_barcode_file):
c = 0
# file should be csv with columns [Name,Direction{1=Forward,0=Reverse},StartSeq,EndSeq]
print("Loading custom barcodes from file {}...".format(custom_barcode_file))
CUSTOM_BARCODES=[]
start_name=''
end_name=''
name=''
custom_barcodes = str(custom_barcode_file)
barcode_dict = {}
with open(custom_barcodes,"r") as f:
for l in f:
c +=1
tokens=l.split(',')
name=tokens[0]
direction = tokens[1]
if direction:
ad_name=name + ' (forward)'
end_name=name+'_rev'
CUSTOM_BARCODES.append(Adapter(ad_name, start_sequence=(name, tokens[2]), end_sequence=(end_name, tokens[3])))
else:
ad_name=name + ' (reverse)'
start_name=name+'_rev'
CUSTOM_BARCODES.append(Adapter(ad_name, start_sequence=(start_name, tokens[2]), end_sequence=(name, tokens[3])))
return CUSTOM_BARCODES