This repository has been archived by the owner on Nov 9, 2023. It is now read-only.
/
test_demultiplex_fasta.py
executable file
·1873 lines (1520 loc) · 88.7 KB
/
test_demultiplex_fasta.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
#!/usr/bin/env python
# file test_demultiplex_fasta.py
__author__ = "Rob Knight"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "William Walters"] # remember to add yourself
__license__ = "GPL"
__version__ = "1.9.0"
__maintainer__ = "William Walters"
__email__ = "william.a.walters@colorado.edu"
from os import close
from os.path import exists, join
from shutil import rmtree
from tempfile import mkdtemp, mkstemp
from skbio.util import create_dir
from unittest import TestCase, main
from skbio.util import remove_files
from qiime.parse import parse_qual_score
from qiime.demultiplex_fasta import (
demultiplex_sequences, assign_seqs, check_map, get_ids_bcs_added_field,
get_bc_lens, process_log_data, process_bc_freqs,
get_added_demultiplex_field, get_exact_bc_matches, attempt_bc_correction,
get_curr_bc_added_field, get_demultiplex_data, write_qual_line,
write_fasta_line, get_label_line, initialize_log_data,
get_output_ids, assign_seqs, process_files_and_demultiplex_sequences
)
class FakeOutFile(object):
def __init__(self, name="test_file"):
self.data = ""
self.name = name
def write(self, s):
self.data += s
class TopLevelTests(TestCase):
"""Tests of top-level functions"""
def setUp(self):
""" Set up test data, output dir for unit tests """
self.valid_mapping_data_golay = valid_mapping_data_golay
self.valid_mapping_data_golay_upper = valid_mapping_data_golay_upper
self.valid_mapping_data_var_len_bcs = valid_mapping_data_var_len_bcs
self.valid_mapping_data_no_bcs_added_demultiplex =\
valid_mapping_data_no_bcs_added_demultiplex
self.valid_mapping_data_bcs_and_added_demultiplex =\
valid_mapping_data_bcs_and_added_demultiplex
self.invalid_mapping_data_golay_header =\
invalid_mapping_data_golay_header
self.invalid_mapping_data_golay_dna =\
invalid_mapping_data_golay_dna
self.invalid_mapping_data_golay_dup_bcs =\
invalid_mapping_data_golay_dup_bcs
self.invalid_mapping_data_golay_dup_sids =\
invalid_mapping_data_golay_dup_sids
self.invalid_mapping_data_no_bcs_added_demultiplex =\
invalid_mapping_data_no_bcs_added_demultiplex
self.invalid_mapping_data_bcs_added_demultiplex =\
invalid_mapping_data_bcs_added_demultiplex
self.invalid_mapping_data_golay_missing_bc =\
invalid_mapping_data_golay_missing_bc
self.expected_formatted_log_data_no_qual =\
expected_formatted_log_data_no_qual
self.expected_formatted_log_data_with_qual =\
expected_formatted_log_data_with_qual
self.valid_mapping_data_no_bcs_no_added_demultiplex =\
valid_mapping_data_no_bcs_no_added_demultiplex
self.valid_fasta_file_no_errors = valid_fasta_file_no_errors
self.valid_qual_file_no_errors = valid_qual_file_no_errors
self.valid_fasta_file_with_bc_errors = valid_fasta_file_with_bc_errors
self.sample_correct_mapping_data = sample_correct_mapping_data
self.sample_fasta_file = sample_fasta_file
self.sample_qual_file = sample_qual_file
self.output_dir = mkdtemp()
self.output_dir += '/'
create_dir(self.output_dir)
fd, self.correct_mapping_fp = mkstemp(
prefix='correct_mapping_',
suffix='.txt')
close(fd)
map_file = open(self.correct_mapping_fp, 'w')
map_file.write(self.sample_correct_mapping_data)
map_file.close()
fd, self.sample_fasta_fp = mkstemp(
prefix='sample_fasta_',
suffix='.fna')
close(fd)
sample_fasta = open(self.sample_fasta_fp, 'w')
sample_fasta.write(self.sample_fasta_file)
sample_fasta.close()
fd, self.sample_qual_fp = mkstemp(
prefix='sample_qual_',
suffix='.qual')
close(fd)
sample_qual = open(self.sample_qual_fp, 'w')
sample_qual.write(self.sample_qual_file)
sample_qual.close()
self._files_to_remove =\
[self.correct_mapping_fp, self.sample_fasta_fp,
self.sample_qual_fp]
def tearDown(self):
if self._files_to_remove:
remove_files(self._files_to_remove)
if exists(self.output_dir):
rmtree(self.output_dir)
def test_process_files_and_demultiplex_sequences(self):
""" Overall IO/functionality test """
process_files_and_demultiplex_sequences(self.correct_mapping_fp,
[self.sample_fasta_fp], [self.sample_qual_fp],
output_dir=self.output_dir, write_unassigned_reads=True,
save_barcode_frequencies=True)
log_file = open(join(self.output_dir, "demultiplex_fasta.log"), "U")
log_lines = [line for line in log_file]
log_file.close()
bc_freqs_f = open(join(self.output_dir, "barcode_freqs.txt"), "U")
bc_freqs = set([line for line in bc_freqs_f])
bc_freqs_f.close()
fasta_seqs_f = open(join(self.output_dir, "demultiplexed_seqs.fna"),
"U")
fasta_lines = [line for line in fasta_seqs_f]
fasta_seqs_f.close()
qual_seqs_f = open(join(self.output_dir, "demultiplexed_seqs.qual"),
"U")
qual_lines = [line for line in qual_seqs_f]
qual_seqs_f.close()
unassigned_fna_f = open(join(self.output_dir, "unassigned_seqs.fna"),
"U")
unassigned_fna_lines = [line for line in unassigned_fna_f]
unassigned_fna_f.close()
unassigned_qual_f = open(join(self.output_dir, "unassigned_seqs.qual"),
"U")
unassigned_qual_line = [line for line in unassigned_qual_f]
unassigned_qual_f.close()
expected_log_lines = [
'Total sequences in input files:\t4\n', 'Retain barcode:\tFalse\n',
'Barcode type:\tgolay_12\n',
'Max barcode error/mismatches allowed:\t0.5\n',
'Starting sequence identifier:\t1\n',
'Write unassigned reads:\tTrue\n',
'Disable barcode correction:\tFalse\n',
'Added demultiplex field:\tNone\n',
'Save barcode frequencies:\tFalse\n', '\n',
'Barcodes corrected/not corrected:\t0/1\n',
'Number of samples in mapping file:\t3\n',
'Sample count min/max/mean:\t1 / 1 / 1.00\n',
'Sample\tSequence Count\tBarcode/Added Demultiplex\n',
'PC.354\t1\tAGCACGAGCCTA\n', 'PC.356\t1\tACAGACCACTCA\n',
'PC.355\t1\tAACTCGTCGATG\n', 'Seqs written\t3\n',
'Percent of input seqs written\t0.75']
# Use set() to avoid order issues with unit tests.
expected_bc_freqs = set(['Barcode frequencies\n',
'ACCCCCCACTCA\t1\n', 'AACTCGTCGATG\t1\n',
'AGCACGAGCCTA\t1\n', 'ACAGACCACTCA\t1'])
expected_fasta_lines = [
'>PC.354_1 ABCD0001 orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0\n',
'CAGGACGAGACGAGGTT\n', '>PC.355_2 EFGH0002 orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n',
'CCAGATTACGAGATTA\n', '>PC.356_3 IJKL0003 orig_bc=ACAGACCACTCA new_bc=ACAGACCACTCA bc_diffs=0\n',
'GACCGATTACGATAACG\n']
expected_qual_lines = [
'>PC.354_1 ABCD0001 orig_bc=AGCACGAGCCTA new_bc=AGCACGAGCCTA bc_diffs=0\n',
'30 26 11 11 29 20 19 16 24 17 29 28 11 27 14 24 24\n',
'>PC.355_2 EFGH0002 orig_bc=AACTCGTCGATG new_bc=AACTCGTCGATG bc_diffs=0\n',
'12 14 27 23 22 19 24 18 19 20 28 10 17 14 17 13\n',
'>PC.356_3 IJKL0003 orig_bc=ACAGACCACTCA new_bc=ACAGACCACTCA bc_diffs=0\n',
'10 20 16 20 25 27 22 28 16 22 16 18 12 13 16 25 17\n']
expected_unassigned_fna_lines = [
'>Unassigned_4 nomatchingBC orig_bc=ACCCCCCACTCA new_bc=GTCCCCCACTGA bc_diffs=3\n',
'ACCCCCCACTCAGACCGATTACGATAACG\n']
expected_unassigned_qual_line = [
'>Unassigned_4 nomatchingBC orig_bc=ACCCCCCACTCA new_bc=GTCCCCCACTGA bc_diffs=3\n',
'30 27 11 16 30 19 13 19 16 15 24 12 10 20 16 20 25 27 22 28 16 22 16 18 12 13 16 25 17\n']
# Skips first few lines that point to tmp filepaths
self.assertEqual(log_lines[5:], expected_log_lines)
self.assertEqual(bc_freqs, expected_bc_freqs)
self.assertEqual(fasta_lines, expected_fasta_lines)
self.assertEqual(qual_lines, expected_qual_lines)
self.assertEqual(unassigned_fna_lines, expected_unassigned_fna_lines)
self.assertEqual(unassigned_qual_line, expected_unassigned_qual_line)
def test_check_map(self):
""" Properly returns data with valid input """
header, mapping_data = check_map(self.valid_mapping_data_golay)
expected_header =\
['SampleID',
'BarcodeSequence',
'LinkerPrimerSequence',
'Description']
expected_mapping_data =\
[['s1', 'AACTCGTCGATG', 'ATTCGATART', 's1_description'],
['s2', 'agcAGCACTTGT', 'ATTCGATART', 's2_description'],
['s3', 'ACCGCAGAGTCA', 'YATGCTGCCTCCCGTAGGAGT', 's3_description']]
self.assertEquals(header, expected_header)
self.assertEquals(mapping_data, expected_mapping_data)
def test_check_map_errors(self):
""" Properly raises errors with invalid input """
# Bad header
self.assertRaises(ValueError, check_map,
self.invalid_mapping_data_golay_header)
# non DNA characters
self.assertRaises(ValueError, check_map,
self.invalid_mapping_data_golay_dna)
# Duplicate barcodes
self.assertRaises(ValueError, check_map,
self.invalid_mapping_data_golay_dup_bcs)
# Duplicate SampleIDs
self.assertRaises(ValueError, check_map,
self.invalid_mapping_data_golay_dup_sids)
# More than one SampleID, no barcodes or added demultiplex specified
self.assertRaises(ValueError, check_map,
self.valid_mapping_data_no_bcs_added_demultiplex, barcode_type=0)
# No barcodes, added_demultiplex has duplicates
self.assertRaises(ValueError, check_map,
self.invalid_mapping_data_no_bcs_added_demultiplex, barcode_type=0,
added_demultiplex_field="Added_Demultiplex")
# Barcodes plus added demultiplex results in duplications
self.assertRaises(ValueError, check_map,
self.invalid_mapping_data_bcs_added_demultiplex,
added_demultiplex_field="Added_Demultiplex")
# Missing a barcode
self.assertRaises(ValueError, check_map,
self.invalid_mapping_data_golay_missing_bc,
barcode_type="variable_length")
def test_check_map_var_len_bcs(self):
""" Properly handles variable length barcodes """
header, mapping_data = check_map(self.valid_mapping_data_var_len_bcs,
barcode_type="variable_length")
expected_header =\
['SampleID',
'BarcodeSequence',
'LinkerPrimerSequence',
'Description']
expected_mapping_data =\
[['s1', 'AACTCGTCGATG', 'ATTCGATART', 's1_description'],
['s2', 'CACTTGT', 'ATTCGATART', 's2_description'],
['s3', 'ACCGCAGAGTCA', 'YATGCTGCCTCCCGTAGGAGT', 's3_description']]
self.assertEquals(header, expected_header)
self.assertEquals(mapping_data, expected_mapping_data)
def test_check_map_var_len_not_specified(self):
""" Raises error if var len bcs detected but not specified """
self.assertRaises(ValueError, check_map,
self.valid_mapping_data_var_len_bcs)
def test_check_map_added_demultiplex(self):
""" Properly handles no barcodes plus added_demultiplex field """
header, mapping_data = check_map(
self.valid_mapping_data_no_bcs_added_demultiplex,
barcode_type=0, added_demultiplex_field="Added_Demultiplex")
expected_header =\
['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
'Added_Demultiplex', 'Description']
expected_mapping_data =\
[['s1', '', 'ATTCGATART', '1', 's1_description'],
['s2', '', 'ATTCGATART', '2', 's2_description'],
['s3', '', 'YATGCTGCCTCCCGTAGGAGT', '3', 's3_description']]
self.assertEquals(header, expected_header)
self.assertEquals(mapping_data, expected_mapping_data)
def test_check_map_single_sample(self):
""" Properly handles single sample with no demultiplex data"""
header, mapping_data = check_map(
valid_mapping_data_no_bcs_no_added_demultiplex,
barcode_type=0)
expected_header =\
['SampleID',
'BarcodeSequence',
'LinkerPrimerSequence',
'Description']
expected_mapping_data =\
[['s1', '', '', 's1_description']]
self.assertEquals(header, expected_header)
self.assertEquals(mapping_data, expected_mapping_data)
def test_check_map_bcs_and_added_demultiplex(self):
""" Properly handles barcodes plus added_demultiplex field """
# Combinations of bc plus added demultiplex field need to be unique
# but can be duplicated if both options are being used.
header, mapping_data = check_map(
self.valid_mapping_data_bcs_and_added_demultiplex,
barcode_type=4, added_demultiplex_field="Added_Demultiplex")
expected_header =\
['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
'Added_Demultiplex', 'Description']
expected_mapping_data =\
[['s1', 'AAAA', 'ATTCGATART', '1', 's1_description'],
['s2', 'AAAA', 'ATTCGATART', '2', 's2_description'],
['s3', 'CCCC', 'YATGCTGCCTCCCGTAGGAGT', '1', 's3_description']]
self.assertEquals(header, expected_header)
self.assertEquals(mapping_data, expected_mapping_data)
def test_get_ids_bcs_added_field(self):
""" Properly returns list of lists of SampleID/bcs/demultiplex data """
header = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
'Added_Demultiplex', 'Description']
mapping_data = [['s1', 'AAAA', 'ATTCGATART', '1', 's1_description'],
['s2', 'ttTT', 'ATTCGATART', '2', 's2_description'],
['s3', 'CCCC', 'YATGCTGCCTCCCGTAGGAGT', '3', 's3_description']]
actual_ids_bcs_added_field = get_ids_bcs_added_field(header,
mapping_data)
expected_ids_bcs_added_field =\
{('CCCC', ''): 's3', ('AAAA', ''): 's1', ('TTTT', ''): 's2'}
self.assertEqual(actual_ids_bcs_added_field,
expected_ids_bcs_added_field)
def test_get_ids_bcs_added_demultiplex_field(self):
""" Properly returns list of lists of SampleID/bcs/demultiplex data """
header = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
'Added_Demultiplex', 'Description']
mapping_data = [['s1', 'AAAA', 'ATTCGATART', '1', 's1_description'],
['s2', 'TTTT', 'ATTCGATART', '2', 's2_description'],
['s3', 'CCCC', 'YATGCTGCCTCCCGTAGGAGT', '3', 's3_description']]
actual_ids_bcs_added_field = get_ids_bcs_added_field(header,
mapping_data, added_demultiplex_field='Added_Demultiplex')
expected_ids_bcs_added_field =\
{('AAAA', '1'): 's1', ('CCCC', '3'): 's3', ('TTTT', '2'): 's2'}
self.assertEqual(actual_ids_bcs_added_field,
expected_ids_bcs_added_field)
def test_get_ids_bcs_no_bcs(self):
""" Properly returns list of lists of SampleID/bcs/demultiplex data """
header = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence',
'Added_Demultiplex', 'Description']
mapping_data = [['s1', 'AAAA', 'ATTCGATART', '1', 's1_description'],
['s2', 'TTTT', 'ATTCGATART', '2', 's2_description'],
['s3', 'CCCC', 'YATGCTGCCTCCCGTAGGAGT', '3', 's3_description']]
actual_ids_bcs_added_field = get_ids_bcs_added_field(header,
mapping_data, barcode_type=0,
added_demultiplex_field='Added_Demultiplex')
expected_ids_bcs_added_field =\
{('', '2'): 's2', ('', '1'): 's1', ('', '3'): 's3'}
self.assertEqual(actual_ids_bcs_added_field,
expected_ids_bcs_added_field)
def test_get_bc_lens(self):
""" Properly returns lengths of barcodes """
sample_data = {('CCCC', ''): 's3', ('AAAA', ''): 's1',
('TTTT', ''): 's2'}
expected_lens = [4]
actual_lens = get_bc_lens(sample_data)
self.assertEqual(actual_lens, expected_lens)
# Test with multiple lengths
sample_data = {('CCCC', ''): 's3', ('', ''): 's1',
('TTTTT', ''): 's2'}
expected_lens = [5, 4, 0]
actual_lens = get_bc_lens(sample_data)
self.assertEqual(actual_lens, expected_lens)
def test_process_log_data_no_qual(self):
""" Properly processes and formats log data with no qual files """
log_data = {'AAAA': 10, 'TTTT': 20, 'CCCC': 0}
seq_counts = 32
mapping_file = 'test_mapping.txt'
fasta_files = [FakeOutFile(name="fasta1.fna"),
FakeOutFile(name="fasta2.fna")]
qual_files = []
corrected_bc_count = [7, 15]
actual_log_data = process_log_data(log_data, seq_counts, mapping_file,
fasta_files, qual_files, corrected_bc_count)
expected_log_data = self.expected_formatted_log_data_no_qual
self.assertEqual(actual_log_data, expected_log_data)
def test_process_log_data_with_qual(self):
""" Properly processes and formats log data with qual files """
log_data = {'AAAA': 10, 'TTTT': 20, 'CCCC': 0}
seq_counts = 32
mapping_file = 'test_mapping.txt'
fasta_files = [FakeOutFile(name="fasta1.fna")]
qual_files = [FakeOutFile(name="qual1.qual")]
corrected_bc_count = [7, 15]
actual_log_data = process_log_data(log_data, seq_counts, mapping_file,
fasta_files, qual_files, corrected_bc_count, keep_barcode=True,
barcode_type=8, max_bc_errors=0, start_index=1000,
write_unassigned_reads=True, disable_bc_correction=True,
added_demultiplex_field='run_prefix', save_barcode_frequencies=True)
expected_log_data = self.expected_formatted_log_data_with_qual
self.assertEqual(actual_log_data, expected_log_data)
def test_process_bc_freqs(self):
""" Properly sorts barcode frequency from largest to smallest """
bc_freqs = {'AAAA': 20, 'TTTT': 47, 'CCCC': 5, 'GGGG': 0}
actual_freqs = process_bc_freqs(bc_freqs)
expected_freqs = ['TTTT\t47', 'AAAA\t20', 'CCCC\t5', 'GGGG\t0']
self.assertEqual(actual_freqs, expected_freqs)
def test_get_added_demultiplex_field_run_prefix(self):
""" Properly returns added demultiplex data using run_prefix """
ids_bcs_added_field = {("AAAA", "ABC"): "S1", ("TTTT", "239A"): "S2"}
fasta_label = "ABC1234 region=1 length=229"
added_demultiplex_field = "run_prefix"
actual_result = get_added_demultiplex_field(ids_bcs_added_field,
fasta_label, added_demultiplex_field)
expected_result = "ABC"
self.assertEqual(actual_result, expected_result)
def test_get_added_demultiplex_field_run_prefix_no_matches(self):
""" Properly returns None when no match with run_prefix """
ids_bcs_added_field = {("AAAA", "ABC"): "S1", ("TTTT", "239A"): "S2"}
fasta_label = "xxABC1234 region=1 length=229"
added_demultiplex_field = "run_prefix"
actual_result = get_added_demultiplex_field(ids_bcs_added_field,
fasta_label, added_demultiplex_field)
expected_result = None
self.assertEqual(actual_result, expected_result)
def test_get_added_demultiplex_field(self):
""" Properly returns added demultiplex data using field in line """
ids_bcs_added_field = {("AAAA", "2"): "S1", ("TTTT", "1"): "S2"}
fasta_label = "ABC1234 region=1 length=229"
added_demultiplex_field = "region"
actual_result = get_added_demultiplex_field(ids_bcs_added_field,
fasta_label, added_demultiplex_field)
expected_result = "1"
self.assertEqual(actual_result, expected_result)
def test_get_added_demultiplex_field_no_match(self):
""" Properly returns None with no matches to field in line """
ids_bcs_added_field = {("AAAA", "2"): "S1", ("TTTT", "3"): "S2"}
fasta_label = "ABC1234 region=1 length=229"
added_demultiplex_field = "region"
actual_result = get_added_demultiplex_field(ids_bcs_added_field,
fasta_label, added_demultiplex_field)
expected_result = None
self.assertEqual(actual_result, expected_result)
def test_get_exact_bc_matches_hit(self):
""" Returns exact matches to barcodes """
curr_bc = "AAAA"
all_bcs = ["AAAAA", "TTTT", "CC", "AAAA"]
actual_bc = get_exact_bc_matches(curr_bc, all_bcs)
expected_bc = "AAAA"
self.assertEqual(actual_bc, expected_bc)
def test_get_exact_bc_matches_no_hit(self):
""" Returns None if no barcodes match """
curr_bc = "AAAA"
all_bcs = ["AAAAA", "TTTT", "CC"]
actual_bc = get_exact_bc_matches(curr_bc, all_bcs)
expected_bc = None
self.assertEqual(actual_bc, expected_bc)
def test_attempt_bc_correction_exact_match(self):
""" Corrects barcode with exact match to given barcodes """
curr_bc = "AGCAGCACTTGT"
all_bcs = ["AACTCGTCGATG", "AGCAGCACTTGT", "ACAGAGTCGGCT"]
barcode_type = "golay_12"
actual_bc, actual_errs = attempt_bc_correction(curr_bc,
all_bcs, barcode_type)
expected_bc = "AGCAGCACTTGT"
expected_errs = 0
self.assertEqual(actual_bc, expected_bc)
self.assertEqual(actual_errs, expected_errs)
def test_attempt_bc_correction_golay12(self):
""" Corrects barcode using golay correction """
curr_bc = "GGCAGCACTTGT"
all_bcs = ["AACTCGTCGATG", "AGCAGCACTTGT", "ACAGAGTCGGCT"]
barcode_type = "golay_12"
actual_bc, actual_errs = attempt_bc_correction(curr_bc,
all_bcs, barcode_type)
expected_bc = "AGCAGCACTTGT"
expected_errs = 1
self.assertEqual(actual_bc, expected_bc)
self.assertEqual(actual_errs, expected_errs)
def test_attempt_bc_correction_golay12_exceeds_range(self):
""" Returns None, count of errors when exceeds correction range """
# Has 4 changes from a valid golay code
curr_bc = "TCGTGCACTTGT"
all_bcs = ["AGCAGCACTTGT", "ACAGAGTCGGCT"]
barcode_type = "golay_12"
actual_bc, actual_errs = attempt_bc_correction(curr_bc,
all_bcs, barcode_type)
expected_bc = None
expected_errs = 4
self.assertEqual(actual_bc, expected_bc)
self.assertEqual(actual_errs, expected_errs)
def test_attempt_bc_correction_hamming8(self):
""" Corrects barcode using hamming correction """
curr_bc = "AGCAGCAC"
all_bcs = ["AGCAGAAC", "TGCAGTAC", "ACAGAGTC"]
barcode_type = "hamming_8"
actual_bc, actual_errs = attempt_bc_correction(curr_bc,
all_bcs, barcode_type)
expected_bc = "AGCAGAAC"
expected_errs = 0.5
self.assertEqual(actual_bc, expected_bc)
self.assertEqual(actual_errs, expected_errs)
def test_attempt_bc_correction_generic(self):
""" Corrects barcode using generic correction """
curr_bc = "GGCAGCACTA"
all_bcs = ["AACTCGTCGA", "AGCAGCACTT", "ACAGAGTCGG"]
barcode_type = 10
actual_bc, actual_errs = attempt_bc_correction(curr_bc,
all_bcs, barcode_type)
expected_bc = "AGCAGCACTT"
expected_errs = 2
self.assertEqual(actual_bc, expected_bc)
self.assertEqual(actual_errs, expected_errs)
def test_attempt_bc_correction_no_barcode(self):
""" Returns empty string, no errors for zero length barcode """
curr_bc = ""
all_bcs = [""]
barcode_type = 0
actual_bc, actual_errs = attempt_bc_correction(curr_bc,
all_bcs, barcode_type)
expected_bc = ""
expected_errs = 0
self.assertEqual(actual_bc, expected_bc)
self.assertEqual(actual_errs, expected_errs)
def test_get_curr_bc_added_field_barcode_only(self):
""" Gets corrected barcode, no added demultiplex field """
curr_bc = "GGCAGCACTTGT"
ids_bcs_added_field = {("AACTCGTCGATG", ""): "s1",
("AGCAGCACTTGT", ""): "s2", ("ACAGAGTCGGCT", ""): "s3"}
fasta_label = "123ABC region=1 length=255"
all_bcs = ["AACTCGTCGATG", "AGCAGCACTTGT", "ACAGAGTCGGCT"]
barcode_type = "golay_12",
disable_bc_correction = False
added_demultiplex_field = None
corrected_bc, num_errors, added_field =\
get_curr_bc_added_field(curr_bc, ids_bcs_added_field, fasta_label,
all_bcs, barcode_type, disable_bc_correction, added_demultiplex_field)
expected_corrected_bc = "AGCAGCACTTGT"
expected_num_errors = 1
expected_added_field = None
self.assertEqual(corrected_bc, expected_corrected_bc)
self.assertEqual(num_errors, expected_num_errors)
self.assertEqual(added_field, expected_added_field)
def test_get_curr_bc_added_field_barcode_only_disabled_correction(self):
""" Returns None when no exact match and correction disabled """
curr_bc = "GGCAGCACTTGT"
ids_bcs_added_field = {("AACTCGTCGATG", ""): "s1",
("AGCAGCACTTGT", ""): "s2", ("ACAGAGTCGGCT", ""): "s3"}
fasta_label = "123ABC region=1 length=255"
all_bcs = ["AACTCGTCGATG", "AGCAGCACTTGT", "ACAGAGTCGGCT"]
barcode_type = "golay_12",
disable_bc_correction = True
added_demultiplex_field = None
corrected_bc, num_errors, added_field =\
get_curr_bc_added_field(curr_bc, ids_bcs_added_field, fasta_label,
all_bcs, barcode_type, disable_bc_correction, added_demultiplex_field)
expected_corrected_bc = None
expected_num_errors = 0
expected_added_field = None
self.assertEqual(corrected_bc, expected_corrected_bc)
self.assertEqual(num_errors, expected_num_errors)
self.assertEqual(added_field, expected_added_field)
def test_get_curr_bc_added_field_barcode_only_no_errs_no_correction(self):
""" Returns barcode with exact match, no error correction """
curr_bc = "AGCAGCACTTGT"
ids_bcs_added_field = {("AACTCGTCGATG", ""): "s1",
("AGCAGCACTTGT", ""): "s2", ("ACAGAGTCGGCT", ""): "s3"}
fasta_label = "123ABC region=1 length=255"
all_bcs = ["AACTCGTCGATG", "AGCAGCACTTGT", "ACAGAGTCGGCT"]
barcode_type = "golay_12",
disable_bc_correction = True
added_demultiplex_field = None
corrected_bc, num_errors, added_field =\
get_curr_bc_added_field(curr_bc, ids_bcs_added_field, fasta_label,
all_bcs, barcode_type, disable_bc_correction, added_demultiplex_field)
expected_corrected_bc = "AGCAGCACTTGT"
expected_num_errors = 0
expected_added_field = None
self.assertEqual(corrected_bc, expected_corrected_bc)
self.assertEqual(num_errors, expected_num_errors)
self.assertEqual(added_field, expected_added_field)
def test_get_curr_bc_added_field_bc_and_added_field(self):
""" Gets corrected barcode and added demultiplex field data """
curr_bc = "GGCAGCACTTGT"
ids_bcs_added_field = {("AACTCGTCGATG", "123"): "s1",
("AGCAGCACTTGT", "123"): "s2", ("ACAGAGTCGGCT", "ABCD"): "s3"}
fasta_label = "123ABC region=1 length=255"
all_bcs = ["AACTCGTCGATG", "AGCAGCACTTGT", "ACAGAGTCGGCT"]
barcode_type = "golay_12",
disable_bc_correction = False
added_demultiplex_field = 'run_prefix'
corrected_bc, num_errors, added_field =\
get_curr_bc_added_field(curr_bc, ids_bcs_added_field, fasta_label,
all_bcs, barcode_type, disable_bc_correction, added_demultiplex_field)
expected_corrected_bc = "AGCAGCACTTGT"
expected_num_errors = 1
expected_added_field = "123"
self.assertEqual(corrected_bc, expected_corrected_bc)
self.assertEqual(num_errors, expected_num_errors)
self.assertEqual(added_field, expected_added_field)
def test_get_curr_bc_added_field_bc_and_added_field_no_hit(self):
""" Gets corrected barcode and no matches to added demultiplex field"""
curr_bc = ""
ids_bcs_added_field = {("", "1"): "s1",
("", "2"): "s2", ("", "3"): "s3"}
fasta_label = "123ABC region=1 length=255"
all_bcs = [""]
barcode_type = 0,
disable_bc_correction = False
added_demultiplex_field = 'region'
corrected_bc, num_errors, added_field =\
get_curr_bc_added_field(curr_bc, ids_bcs_added_field, fasta_label,
all_bcs, barcode_type, disable_bc_correction, added_demultiplex_field)
expected_corrected_bc = ""
expected_num_errors = 0
expected_added_field = "1"
self.assertEqual(corrected_bc, expected_corrected_bc)
self.assertEqual(num_errors, expected_num_errors)
self.assertEqual(added_field, expected_added_field)
def test_get_curr_bc_added_field_added_field_only(self):
""" Gets data with no barcode, added field only """
curr_bc = "GGCAGCACTTGT"
ids_bcs_added_field = {("AACTCGTCGATG", "123"): "s1",
("AGCAGCACTTGT", "123"): "s2", ("ACAGAGTCGGCT", "ABCD"): "s3"}
fasta_label = "123ABC region=1 length=255"
all_bcs = ["AACTCGTCGATG", "AGCAGCACTTGT", "ACAGAGTCGGCT"]
barcode_type = "golay_12",
disable_bc_correction = False
added_demultiplex_field = 'run_prefix'
corrected_bc, num_errors, added_field =\
get_curr_bc_added_field(curr_bc, ids_bcs_added_field, fasta_label,
all_bcs, barcode_type, disable_bc_correction, added_demultiplex_field)
expected_corrected_bc = "AGCAGCACTTGT"
expected_num_errors = 1
expected_added_field = "123"
self.assertEqual(corrected_bc, expected_corrected_bc)
self.assertEqual(num_errors, expected_num_errors)
self.assertEqual(added_field, expected_added_field)
def test_get_demultiplex_data_fixed_length_bcs(self):
""" Gets bc/added data, handles fixed length barcodes """
ids_bcs_added_field = {("AACTCGTCGATG", ""): "s1",
("AGCAGCACTTGT", ""): "s2", ("ACAGAGTCGGCT", ""): "s3"}
fasta_label = "123ABC region=1 length=255"
fasta_seq = "TGCAGCACTTGTACAGATTAGACCGAGATTACGAGATTACCAAGAT"
bc_lens = [12]
all_bcs = ["AACTCGTCGATG", "AGCAGCACTTGT", "ACAGAGTCGGCT"]
barcode_type = "golay_12"
max_bc_errors = 1.5
disable_bc_correction = False
added_demultiplex_field = None
curr_bc, corrected_bc, num_errors, added_field =\
get_demultiplex_data(ids_bcs_added_field, fasta_label, fasta_seq,
bc_lens, all_bcs, barcode_type, max_bc_errors, disable_bc_correction,
added_demultiplex_field)
expected_curr_bc = "TGCAGCACTTGT"
expected_corrected_bc = "AGCAGCACTTGT"
expected_num_errors = 1
expected_added_field = None
self.assertEqual(curr_bc, expected_curr_bc)
self.assertEqual(corrected_bc, expected_corrected_bc)
self.assertEqual(num_errors, expected_num_errors)
self.assertEqual(added_field, expected_added_field)
def test_get_demultiplex_data_variable_length_bcs(self):
""" Gets bc/added data, handles variable length barcodes """
# Should return on first hit, from largest to shortest barcode
ids_bcs_added_field = {("AACTCGT", ""): "s1",
("AGCAGCACTTGT", ""): "s2", ("AGCAG", ""): "s3"}
fasta_label = "123ABC region=1 length=255"
fasta_seq = "AGCAGCACTTGTACAGATTAGACCGAGATTACGAGATTACCAAGAT"
bc_lens = [12, 7, 5]
all_bcs = ["AACTCGT", "AGCAGCACTTGT", "AGCAG"]
barcode_type = "variable_length"
max_bc_errors = 1.5
disable_bc_correction = True
added_demultiplex_field = None
curr_bc, corrected_bc, num_errors, added_field =\
get_demultiplex_data(ids_bcs_added_field, fasta_label, fasta_seq,
bc_lens, all_bcs, barcode_type, max_bc_errors, disable_bc_correction,
added_demultiplex_field)
expected_curr_bc = "AGCAGCACTTGT"
expected_corrected_bc = "AGCAGCACTTGT"
expected_num_errors = 0
expected_added_field = None
self.assertEqual(curr_bc, expected_curr_bc)
self.assertEqual(corrected_bc, expected_corrected_bc)
self.assertEqual(num_errors, expected_num_errors)
self.assertEqual(added_field, expected_added_field)
def test_get_demultiplex_data_variable_length_bcs_added_field(self):
""" Gets bc/added data, handles var length barcodes plus added field"""
# Should return shortest barcode, as this has the match to the added
# field
ids_bcs_added_field = {("AACTCGT", "1"): "s1",
("AGCAGCACTTGT", "2"): "s2", ("AGCAG", "1"): "s3"}
fasta_label = "123ABC region=1 length=255"
fasta_seq = "AGCAGCACTTGTACAGATTAGACCGAGATTACGAGATTACCAAGAT"
bc_lens = [12, 7, 5]
all_bcs = ["AACTCGT", "AGCAGCACTTGT", "AGCAG"]
barcode_type = "variable_length"
max_bc_errors = 1.5
disable_bc_correction = True
added_demultiplex_field = 'region'
curr_bc, corrected_bc, num_errors, added_field =\
get_demultiplex_data(ids_bcs_added_field, fasta_label, fasta_seq,
bc_lens, all_bcs, barcode_type, max_bc_errors, disable_bc_correction,
added_demultiplex_field)
expected_curr_bc = "AGCAG"
expected_corrected_bc = "AGCAG"
expected_num_errors = 0
expected_added_field = '1'
self.assertEqual(curr_bc, expected_curr_bc)
self.assertEqual(corrected_bc, expected_corrected_bc)
self.assertEqual(num_errors, expected_num_errors)
self.assertEqual(added_field, expected_added_field)
def test_write_qual_line_short_seq(self):
""" Properly formats, writes qual score label/line for short seq """
demultiplexed_qual_f = FakeOutFile()
qual_seq = [25, 24, 22, 24, 24, 24, 25, 30, 23, 22, 22, 24, 25]
label_line = "sample3_1 ABCD1234"
keep_barcode = False
bc_len = 4
write_qual_line(demultiplexed_qual_f, qual_seq, label_line,
keep_barcode, bc_len)
expected_data = '>sample3_1 ABCD1234\n24 24 25 30 23 22 22 24 25\n'
self.assertEqual(demultiplexed_qual_f.data, expected_data)
def test_write_qual_line_short_seq_retains_bc(self):
""" Properly formats, writes qual score, retains BC segment """
demultiplexed_qual_f = FakeOutFile()
qual_seq = [25, 24, 22, 24, 24, 24, 25, 30, 23, 22, 22, 24, 25]
label_line = "sample3_1 ABCD1234"
keep_barcode = True
bc_len = 4
write_qual_line(demultiplexed_qual_f, qual_seq, label_line,
keep_barcode, bc_len)
expected_data =\
'>sample3_1 ABCD1234\n25 24 22 24 24 24 25 30 23 22 22 24 25\n'
self.assertEqual(demultiplexed_qual_f.data, expected_data)
def test_write_qual_line_long_seq(self):
""" Properly formats, writes qual score label/line for long seq """
demultiplexed_qual_f = FakeOutFile()
qual_seq = [25, 24, 22, 24, 24, 24, 25, 30, 23, 22, 22, 24, 25,
14, 25, 27, 29, 30, 14, 10, 1, 23, 24, 27, 28, 30, 22, 24, 21,
24, 22, 21, 15, 17, 17, 15, 22, 13, 11, 10, 22, 24, 27, 28, 30,
14, 25, 27, 29, 30, 14, 10, 1, 23, 24, 27, 28, 30, 22, 24, 21,
14, 25, 27, 29, 30, 14, 10, 1, 23, 24, 27, 28, 30, 22, 24, 21]
label_line = "sample3_1 ABCD1234"
keep_barcode = False
bc_len = 4
write_qual_line(demultiplexed_qual_f, qual_seq, label_line,
keep_barcode, bc_len)
expected_data = '>sample3_1 ABCD1234\n24 24 25 30 23 22 22 24 25 14 25 27 29 30 14 10 1 23 24 27 28 30 22 24 21 24 22 21 15 17 17 15 22 13 11 10 22 24 27 28 30 14 25 27 29 30 14 10 1 23 24 27 28 30 22 24 21 14 25 27\n29 30 14 10 1 23 24 27 28 30 22 24 21\n'
self.assertEqual(demultiplexed_qual_f.data, expected_data)
def test_write_qual_line_long_seq_retain_bc(self):
""" Properly formats, writes qual long qual score with bc """
demultiplexed_qual_f = FakeOutFile()
qual_seq = [25, 24, 22, 24, 24, 24, 25, 30, 23, 22, 22, 24, 25,
14, 25, 27, 29, 30, 14, 10, 1, 23, 24, 27, 28, 30, 22, 24, 21,
24, 22, 21, 15, 17, 17, 15, 22, 13, 11, 10, 22, 24, 27, 28, 30,
14, 25, 27, 29, 30, 14, 10, 1, 23, 24, 27, 28, 30, 22, 24, 21,
14, 25, 27, 29, 30, 14, 10, 1, 23, 24, 27, 28, 30, 22, 24, 21]
label_line = "sample3_1 ABCD1234"
keep_barcode = True
bc_len = 4
write_qual_line(demultiplexed_qual_f, qual_seq, label_line,
keep_barcode, bc_len)
expected_data = '>sample3_1 ABCD1234\n25 24 22 24 24 24 25 30 23 22 22 24 25 14 25 27 29 30 14 10 1 23 24 27 28 30 22 24 21 24 22 21 15 17 17 15 22 13 11 10 22 24 27 28 30 14 25 27 29 30 14 10 1 23 24 27 28 30 22 24\n21 14 25 27 29 30 14 10 1 23 24 27 28 30 22 24 21\n'
self.assertEqual(demultiplexed_qual_f.data, expected_data)
def test_write_fasta_line(self):
""" Properly formats, write fasta label/line """
demultiplexed_seqs_f = FakeOutFile()
fasta_seq = "ACTAGACCTACAGGATACCATAGGACCAGATTTACA"
label_line = "Sample1_213 ABCD1234"
keep_barcode = False
bc_len = 4
write_fasta_line(demultiplexed_seqs_f, fasta_seq, label_line,
keep_barcode, bc_len)
expected_data = ">Sample1_213 ABCD1234\nGACCTACAGGATACCATAGGACCAGATTTACA\n"
self.assertEqual(demultiplexed_seqs_f.data, expected_data)
def test_write_fasta_line_retain_bc(self):
""" Properly formats, write fasta label/line, retains bc seqs """
demultiplexed_seqs_f = FakeOutFile()
fasta_seq = "ACTAGACCTACAGGATACCATAGGACCAGATTTACA"
label_line = "Sample1_213 ABCD1234"
keep_barcode = True
bc_len = 4
write_fasta_line(demultiplexed_seqs_f, fasta_seq, label_line,
keep_barcode, bc_len)
expected_data = ">Sample1_213 ABCD1234\nACTAGACCTACAGGATACCATAGGACCAGATTTACA\n"
self.assertEqual(demultiplexed_seqs_f.data, expected_data)
def test_get_label_line(self):
""" Properly formats fasta label """
sample_id = "Sample1"
fasta_label = "ABCD1234 region=1 length=254"
bc = "AAAA"
corrected_bc = "AAAT"
num_errors = 1
actual_label = get_label_line(sample_id, fasta_label, bc, corrected_bc,
num_errors)
expected_label = "Sample1 ABCD1234 orig_bc=AAAA new_bc=AAAT bc_diffs=1"
self.assertEqual(actual_label, expected_label)
def test_initialize_log_data(self):
""" Properly initializes dict of zero counts for sample IDs """
ids_bcs_added_field = {('AAAA', ''): 's1', ('TTTT', ''): 's2'}
actual_log_data = initialize_log_data(ids_bcs_added_field)
expected_log_data = {'TTTT,s2': 0, 'AAAA,s1': 0}
self.assertEqual(actual_log_data, expected_log_data)
# Handles added demultiplex field data
ids_bcs_added_field = {('AAAA', '1'): 's1', ('TTTT', '2'): 's2'}
actual_log_data = initialize_log_data(ids_bcs_added_field)
expected_log_data = {'TTTT,2,s2': 0, 'AAAA,1,s1': 0}
self.assertEqual(actual_log_data, expected_log_data)
def test_get_output_ids_correct_bc(self):
""" Properly formats SampleIDs/enumeration for writing seqs """
ids_bcs_added_field = {('AAAA', ''): 's1', ('TTTT', ''): 's2'}
corrected_bc = 'AAAA'
num_errors = 0
added_field = None
sample_id, log_id, bc_corrected_flag =\
get_output_ids(ids_bcs_added_field, corrected_bc, num_errors,
added_field)
expected_sample_id = 's1_1'
expected_log_id = 'AAAA,s1'
expected_bc_corrected_flag = None
self.assertEqual(sample_id, expected_sample_id)
self.assertEqual(log_id, expected_log_id)
self.assertEqual(bc_corrected_flag, expected_bc_corrected_flag)
def test_get_output_ids_correct_bc_with_correction(self):
""" Properly formats SampleIDs/enumeration for writing seqs """
ids_bcs_added_field = {('AAAA', ''): 's1', ('TTTT', ''): 's2'}
corrected_bc = 'AAAA'
num_errors = 1
added_field = None