forked from lh3/seqtk
-
Notifications
You must be signed in to change notification settings - Fork 0
/
seqtk.c
1716 lines (1627 loc) · 53 KB
/
seqtk.c
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
/* The MIT License
Copyright (c) 2008-2016 Broad Institute
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
#include <stdio.h>
#include <ctype.h>
#include <stdlib.h>
#include <stdint.h>
#include <inttypes.h>
#include <zlib.h>
#include <string.h>
#include <unistd.h>
#include <limits.h>
#include <assert.h>
#include <math.h>
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
typedef struct {
int n, m;
uint64_t *a;
} reglist_t;
#include "khash.h"
KHASH_MAP_INIT_STR(reg, reglist_t)
KHASH_SET_INIT_INT64(64)
typedef kh_reg_t reghash_t;
reghash_t *stk_reg_read(const char *fn)
{
reghash_t *h = kh_init(reg);
gzFile fp;
kstream_t *ks;
int dret;
kstring_t *str;
// read the list
fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) return 0;
ks = ks_init(fp);
str = calloc(1, sizeof(kstring_t));
while (ks_getuntil(ks, 0, str, &dret) >= 0) {
int beg = -1, end = -1;
reglist_t *p;
khint_t k = kh_get(reg, h, str->s);
if (k == kh_end(h)) {
int ret;
char *s = strdup(str->s);
k = kh_put(reg, h, s, &ret);
memset(&kh_val(h, k), 0, sizeof(reglist_t));
}
p = &kh_val(h, k);
if (dret != '\n') {
if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
beg = atoi(str->s);
if (dret != '\n') {
if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
end = atoi(str->s);
if (end < 0) end = -1;
}
}
}
}
// skip the rest of the line
if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column
if (beg < 0) beg = 0, end = INT_MAX;
if (p->n == p->m) {
p->m = p->m? p->m<<1 : 4;
p->a = realloc(p->a, p->m * 8);
}
p->a[p->n++] = (uint64_t)beg<<32 | end;
}
ks_destroy(ks);
gzclose(fp);
free(str->s); free(str);
return h;
}
void stk_reg_destroy(reghash_t *h)
{
khint_t k;
if (h == 0) return;
for (k = 0; k < kh_end(h); ++k) {
if (kh_exist(h, k)) {
free(kh_val(h, k).a);
free((char*)kh_key(h, k));
}
}
kh_destroy(reg, h);
}
/* constant table */
unsigned char seq_nt16_table[256] = {
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15 /*'-'*/,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
15,15, 5, 6, 8,15, 7, 9, 0,10,15,15, 15,15,15,15,
15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
15,15, 5, 6, 8,15, 7, 9, 0,10,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
};
unsigned char seq_nt6_table[256] = {
0, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 1, 5, 2, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 1, 5, 2, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5
};
char *seq_nt16_rev_table = "XACMGRSVTWYHKDBN";
unsigned char seq_nt16to4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
unsigned char seq_nt16comp_table[] = { 0, 8, 4, 12, 2, 10, 9, 14, 1, 6, 5, 13, 3, 11, 7, 15 };
int bitcnt_table[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };
char comp_tab[] = {
0, 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, 'T', 'V', 'G', 'H', 'E', 'F', 'C', 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
'P', 'Q', 'Y', 'S', 'A', 'A', 'B', 'W', 'X', 'R', 'Z', 91, 92, 93, 94, 95,
64, 't', 'v', 'g', 'h', 'e', 'f', 'c', 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
'p', 'q', 'y', 's', 'a', 'a', 'b', 'w', 'x', 'r', 'z', 123, 124, 125, 126, 127
};
static void stk_printstr(const kstring_t *s, unsigned line_len)
{
if (line_len != UINT_MAX && line_len != 0) {
int i, rest = s->l;
for (i = 0; i < s->l; i += line_len, rest -= line_len) {
putchar('\n');
if (rest > line_len) fwrite(s->s + i, 1, line_len, stdout);
else fwrite(s->s + i, 1, rest, stdout);
}
putchar('\n');
} else {
putchar('\n');
puts(s->s);
}
}
static inline void stk_printseq_renamed(const kseq_t *s, int line_len, const char *prefix, int64_t n)
{
putchar(s->qual.l? '@' : '>');
if (n >= 0) {
if (prefix) fputs(prefix, stdout);
printf("%lld", (long long)n);
} else fputs(s->name.s, stdout);
if (s->comment.l) {
putchar(' '); fputs(s->comment.s, stdout);
}
stk_printstr(&s->seq, line_len);
if (s->qual.l) {
putchar('+');
stk_printstr(&s->qual, line_len);
}
}
static inline void stk_printseq(const kseq_t *s, int line_len)
{
stk_printseq_renamed(s, line_len, 0, -1);
}
/*
64-bit Mersenne Twister pseudorandom number generator. Adapted from:
http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/VERSIONS/C-LANG/mt19937-64.c
which was written by Takuji Nishimura and Makoto Matsumoto and released
under the 3-clause BSD license.
*/
typedef uint64_t krint64_t;
struct _krand_t;
typedef struct _krand_t krand_t;
#define KR_NN 312
#define KR_MM 156
#define KR_UM 0xFFFFFFFF80000000ULL /* Most significant 33 bits */
#define KR_LM 0x7FFFFFFFULL /* Least significant 31 bits */
struct _krand_t {
int mti;
krint64_t mt[KR_NN];
};
static void kr_srand0(krint64_t seed, krand_t *kr)
{
kr->mt[0] = seed;
for (kr->mti = 1; kr->mti < KR_NN; ++kr->mti)
kr->mt[kr->mti] = 6364136223846793005ULL * (kr->mt[kr->mti - 1] ^ (kr->mt[kr->mti - 1] >> 62)) + kr->mti;
}
krand_t *kr_srand(krint64_t seed)
{
krand_t *kr;
kr = malloc(sizeof(krand_t));
kr_srand0(seed, kr);
return kr;
}
krint64_t kr_rand(krand_t *kr)
{
krint64_t x;
static const krint64_t mag01[2] = { 0, 0xB5026F5AA96619E9ULL };
if (kr->mti >= KR_NN) {
int i;
if (kr->mti == KR_NN + 1) kr_srand0(5489ULL, kr);
for (i = 0; i < KR_NN - KR_MM; ++i) {
x = (kr->mt[i] & KR_UM) | (kr->mt[i+1] & KR_LM);
kr->mt[i] = kr->mt[i + KR_MM] ^ (x>>1) ^ mag01[(int)(x&1)];
}
for (; i < KR_NN - 1; ++i) {
x = (kr->mt[i] & KR_UM) | (kr->mt[i+1] & KR_LM);
kr->mt[i] = kr->mt[i + (KR_MM - KR_NN)] ^ (x>>1) ^ mag01[(int)(x&1)];
}
x = (kr->mt[KR_NN - 1] & KR_UM) | (kr->mt[0] & KR_LM);
kr->mt[KR_NN - 1] = kr->mt[KR_MM - 1] ^ (x>>1) ^ mag01[(int)(x&1)];
kr->mti = 0;
}
x = kr->mt[kr->mti++];
x ^= (x >> 29) & 0x5555555555555555ULL;
x ^= (x << 17) & 0x71D67FFFEDA60000ULL;
x ^= (x << 37) & 0xFFF7EEE000000000ULL;
x ^= (x >> 43);
return x;
}
#define kr_drand(_kr) ((kr_rand(_kr) >> 11) * (1.0/9007199254740992.0))
/* quality based trimming with Mott's algorithm */
int stk_trimfq(int argc, char *argv[])
{ // FIXME: when a record with zero length will always be treated as a fasta record
gzFile fp;
kseq_t *seq;
double param = 0.05, q_int2real[128];
int i, c, min_len = 30, left = 0, right = 0, fixed_len = -1;
while ((c = getopt(argc, argv, "l:q:b:e:L:")) >= 0) {
switch (c) {
case 'q': param = atof(optarg); break;
case 'l': min_len = atoi(optarg); break;
case 'b': left = atoi(optarg); break;
case 'e': right = atoi(optarg); break;
case 'L': fixed_len = atoi(optarg); break;
}
}
if (optind == argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk trimfq [options] <in.fq>\n\n");
fprintf(stderr, "Options: -q FLOAT error rate threshold (disabled by -b/-e) [%.2f]\n", param);
fprintf(stderr, " -l INT maximally trim down to INT bp (disabled by -b/-e) [%d]\n", min_len);
fprintf(stderr, " -b INT trim INT bp from left (non-zero to disable -q/-l) [0]\n");
fprintf(stderr, " -e INT trim INT bp from right (non-zero to disable -q/-l) [0]\n");
fprintf(stderr, " -L INT retain at most INT bp from the 5'-end (non-zero to disable -q/-l) [0]\n");
fprintf(stderr, " -Q force FASTQ output\n");
fprintf(stderr, "\n");
return 1;
}
fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
for (i = 0; i < 128; ++i)
q_int2real[i] = pow(10., -(i - 33) / 10.);
while (kseq_read(seq) >= 0) {
int beg, tmp, end;
double s, max;
if (left || right || fixed_len > 0) {
beg = left; end = seq->seq.l - right;
if (beg >= end) beg = end = 0;
if (fixed_len > 0 && end - beg > fixed_len) end = beg + fixed_len;
} else if (seq->qual.l > min_len) {
for (i = 0, beg = tmp = 0, end = seq->qual.l, s = max = 0.; i < seq->qual.l; ++i) {
int q = seq->qual.s[i];
if (q < 36) q = 36;
if (q > 127) q = 127;
s += param - q_int2real[q];
if (s > max) max = s, beg = tmp, end = i + 1;
if (s < 0) s = 0, tmp = i + 1;
}
/* max never set; all low qual, just give first min_len bp */
if (max == 0.) beg = 0, end = min_len;
if (end - beg < min_len) { // window-based
int is, imax;
for (i = 0, is = 0; i < min_len; ++i)
is += seq->qual.s[i] - 33;
for (imax = is, beg = 0; i < seq->qual.l; ++i) {
is += (int)seq->qual.s[i] - seq->qual.s[i - min_len];
if (imax < is) imax = is, beg = i - min_len + 1;
}
end = beg + min_len;
}
} else beg = 0, end = seq->seq.l;
putchar(seq->is_fastq? '@' : '>'); fputs(seq->name.s, stdout);
if (seq->comment.l) {
putchar(' '); puts(seq->comment.s);
} else putchar('\n');
fwrite(seq->seq.s + beg, 1, end - beg, stdout); putchar('\n');
if (seq->is_fastq) {
puts("+");
fwrite(seq->qual.s + beg, 1, end - beg, stdout); putchar('\n');
}
}
kseq_destroy(seq);
gzclose(fp);
return 0;
}
/* composition */
int stk_comp(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq;
int l, c, upper_only = 0;
reghash_t *h = 0;
reglist_t dummy;
while ((c = getopt(argc, argv, "ur:")) >= 0) {
switch (c) {
case 'u': upper_only = 1; break;
case 'r': h = stk_reg_read(optarg); break;
}
}
if (argc == optind && isatty(fileno(stdin))) {
fprintf(stderr, "Usage: seqtk comp [-u] [-r in.bed] <in.fa>\n\n");
fprintf(stderr, "Output format: chr, length, #A, #C, #G, #T, #2, #3, #4, #CpG, #tv, #ts, #CpG-ts\n");
return 1;
}
fp = optind < argc && strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
dummy.n= dummy.m = 1; dummy.a = calloc(1, 8);
while ((l = kseq_read(seq)) >= 0) {
int i, k;
reglist_t *p = 0;
if (h) {
khint_t k = kh_get(reg, h, seq->name.s);
if (k != kh_end(h)) p = &kh_val(h, k);
} else {
p = &dummy;
dummy.a[0] = l;
}
for (k = 0; p && k < p->n; ++k) {
int beg = p->a[k]>>32, end = p->a[k]&0xffffffff;
int la, lb, lc, na, nb, nc, cnt[11];
if (beg > 0) la = seq->seq.s[beg-1], lb = seq_nt16_table[la], lc = bitcnt_table[lb];
else la = 'a', lb = -1, lc = 0;
na = seq->seq.s[beg]; nb = seq_nt16_table[na]; nc = bitcnt_table[nb];
memset(cnt, 0, 11 * sizeof(int));
for (i = beg; i < end; ++i) {
int is_CpG = 0, a, b, c;
a = na; b = nb; c = nc;
na = seq->seq.s[i+1]; nb = seq_nt16_table[na]; nc = bitcnt_table[nb];
if (b == 2 || b == 10) { // C or Y
if (nb == 4 || nb == 5) is_CpG = 1;
} else if (b == 4 || b == 5) { // G or R
if (lb == 2 || lb == 10) is_CpG = 1;
}
if (upper_only == 0 || isupper(a)) {
if (c > 1) ++cnt[c+2];
if (c == 1) ++cnt[seq_nt16to4_table[b]];
if (b == 10 || b == 5) ++cnt[9];
else if (c == 2) {
++cnt[8];
}
if (is_CpG) {
++cnt[7];
if (b == 10 || b == 5) ++cnt[10];
}
}
la = a; lb = b; lc = c;
}
if (h) printf("%s\t%d\t%d", seq->name.s, beg, end);
else printf("%s\t%d", seq->name.s, l);
for (i = 0; i < 11; ++i) printf("\t%d", cnt[i]);
putchar('\n');
}
fflush(stdout);
}
free(dummy.a);
kseq_destroy(seq);
gzclose(fp);
return 0;
}
int stk_randbase(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq;
int l;
if (argc == 1) {
fprintf(stderr, "Usage: seqtk randbase <in.fa>\n");
return 1;
}
fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
int i;
printf(">%s", seq->name.s);
for (i = 0; i < l; ++i) {
int c, b, a, j, k, m;
b = seq->seq.s[i];
c = seq_nt16_table[b];
a = bitcnt_table[c];
if (a == 2) {
m = (drand48() < 0.5);
for (j = k = 0; j < 4; ++j) {
if ((1<<j & c) == 0) continue;
if (k == m) break;
++k;
}
seq->seq.s[i] = islower(b)? "acgt"[j] : "ACGT"[j];
}
if (i%60 == 0) putchar('\n');
putchar(seq->seq.s[i]);
}
putchar('\n');
}
kseq_destroy(seq);
gzclose(fp);
return 0;
}
int stk_hety(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq;
int l, c, win_size = 50000, n_start = 5, win_step, is_lower_mask = 0;
char *buf;
uint32_t cnt[3];
if (argc == 1) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk hety [options] <in.fa>\n\n");
fprintf(stderr, "Options: -w INT window size [%d]\n", win_size);
fprintf(stderr, " -t INT # start positions in a window [%d]\n", n_start);
fprintf(stderr, " -m treat lowercases as masked\n");
fprintf(stderr, "\n");
return 1;
}
while ((c = getopt(argc, argv, "w:t:m")) >= 0) {
switch (c) {
case 'w': win_size = atoi(optarg); break;
case 't': n_start = atoi(optarg); break;
case 'm': is_lower_mask = 1; break;
}
}
fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
win_step = win_size / n_start;
buf = calloc(win_size, 1);
while ((l = kseq_read(seq)) >= 0) {
int x, i, y, z, next = 0;
cnt[0] = cnt[1] = cnt[2] = 0;
for (i = 0; i <= l; ++i) {
if ((i >= win_size && i % win_step == 0) || i == l) {
if (i == l && l >= win_size) {
for (y = l - win_size; y < next; ++y) --cnt[(int)buf[y % win_size]];
}
if (cnt[1] + cnt[2] > 0)
printf("%s\t%d\t%d\t%.2lf\t%d\t%d\n", seq->name.s, next, i,
(double)cnt[2] / (cnt[1] + cnt[2]) * win_size, cnt[1] + cnt[2], cnt[2]);
next = i;
}
if (i < l) {
y = i % win_size;
c = seq->seq.s[i];
if (is_lower_mask && islower(c)) c = 'N';
c = seq_nt16_table[c];
x = bitcnt_table[c];
if (i >= win_size) --cnt[(int)buf[y]];
buf[y] = z = x > 2? 0 : x == 2? 2 : 1;
++cnt[z];
}
}
}
free(buf);
kseq_destroy(seq);
gzclose(fp);
return 0;
}
/* subseq */
int stk_subseq(int argc, char *argv[])
{
khash_t(reg) *h = kh_init(reg);
gzFile fp;
kseq_t *seq;
int l, i, j, c, is_tab = 0, line = 0;
khint_t k;
while ((c = getopt(argc, argv, "tl:")) >= 0) {
switch (c) {
case 't': is_tab = 1; break;
case 'l': line = atoi(optarg); break;
}
}
if (optind + 2 > argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk subseq [options] <in.fa> <in.bed>|<name.list>\n\n");
fprintf(stderr, "Options: -t TAB delimited output\n");
fprintf(stderr, " -l INT sequence line length [%d]\n\n", line);
fprintf(stderr, "Note: Use 'samtools faidx' if only a few regions are intended.\n\n");
return 1;
}
h = stk_reg_read(argv[optind+1]);
if (h == 0) {
fprintf(stderr, "[E::%s] failed to read the list of regions in file '%s'\n", __func__, argv[optind+1]);
return 1;
}
// subseq
fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream\n", __func__);
return 1;
}
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
reglist_t *p;
k = kh_get(reg, h, seq->name.s);
if (k == kh_end(h)) continue;
p = &kh_val(h, k);
for (i = 0; i < p->n; ++i) {
int beg = p->a[i]>>32, end = p->a[i];
if (beg >= seq->seq.l) {
fprintf(stderr, "[subseq] %s: %d >= %ld\n", seq->name.s, beg, seq->seq.l);
continue;
}
if (end > seq->seq.l) end = seq->seq.l;
if (is_tab == 0) {
printf("%c%s", seq->qual.l == seq->seq.l? '@' : '>', seq->name.s);
if (beg > 0 || (int)p->a[i] != INT_MAX) {
if (end == INT_MAX) {
if (beg) printf(":%d", beg+1);
} else printf(":%d-%d", beg+1, end);
}
if (seq->comment.l) printf(" %s", seq->comment.s);
} else printf("%s\t%d\t", seq->name.s, beg + 1);
if (end > seq->seq.l) end = seq->seq.l;
for (j = 0; j < end - beg; ++j) {
if (is_tab == 0 && (j == 0 || (line > 0 && j % line == 0))) putchar('\n');
putchar(seq->seq.s[j + beg]);
}
putchar('\n');
if (seq->qual.l != seq->seq.l || is_tab) continue;
printf("+");
for (j = 0; j < end - beg; ++j) {
if (j == 0 || (line > 0 && j % line == 0)) putchar('\n');
putchar(seq->qual.s[j + beg]);
}
putchar('\n');
}
}
// free
kseq_destroy(seq);
gzclose(fp);
stk_reg_destroy(h);
return 0;
}
/* mergefa */
int stk_mergefa(int argc, char *argv[])
{
gzFile fp[2];
kseq_t *seq[2];
int i, l, c, is_intersect = 0, is_haploid = 0, qual = 0, is_mask = 0, is_randhet = 0;
uint64_t cnt[5];
while ((c = getopt(argc, argv, "himrq:")) >= 0) {
switch (c) {
case 'i': is_intersect = 1; break;
case 'h': is_haploid = 1; break;
case 'm': is_mask = 1; break;
case 'r': is_randhet = 1; break;
case 'q': qual = atoi(optarg); break;
}
}
if (is_mask && is_intersect) {
fprintf(stderr, "[%s] `-i' and `-h' cannot be applied at the same time.\n", __func__);
return 1;
}
if (optind + 2 > argc) {
fprintf(stderr, "\nUsage: seqtk mergefa [options] <in1.fa> <in2.fa>\n\n");
fprintf(stderr, "Options: -q INT quality threshold [0]\n");
fprintf(stderr, " -i take intersection\n");
fprintf(stderr, " -m convert to lowercase when one of the input base is N\n");
fprintf(stderr, " -r pick a random allele from het\n");
fprintf(stderr, " -h suppress hets in the input\n\n");
return 1;
}
for (i = 0; i < 2; ++i) {
fp[i] = strcmp(argv[optind+i], "-")? gzopen(argv[optind+i], "r") : gzdopen(fileno(stdin), "r");
seq[i] = kseq_init(fp[i]);
}
if (fp[0] == 0 || fp[1] == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
cnt[0] = cnt[1] = cnt[2] = cnt[3] = cnt[4] = 0;
srand48(11);
while (kseq_read(seq[0]) >= 0) {
int min_l, c[2], b[2], is_upper;
kseq_read(seq[1]);
if (strcmp(seq[0]->name.s, seq[1]->name.s))
fprintf(stderr, "[%s] Different sequence names: %s != %s\n", __func__, seq[0]->name.s, seq[1]->name.s);
if (seq[0]->seq.l != seq[1]->seq.l)
fprintf(stderr, "[%s] Unequal sequence length: %ld != %ld\n", __func__, seq[0]->seq.l, seq[1]->seq.l);
min_l = seq[0]->seq.l < seq[1]->seq.l? seq[0]->seq.l : seq[1]->seq.l;
printf(">%s", seq[0]->name.s);
for (l = 0; l < min_l; ++l) {
c[0] = seq[0]->seq.s[l]; c[1] = seq[1]->seq.s[l];
if (seq[0]->qual.l && seq[0]->qual.s[l] - 33 < qual) c[0] = tolower(c[0]);
if (seq[1]->qual.l && seq[1]->qual.s[l] - 33 < qual) c[1] = tolower(c[1]);
if (is_intersect) is_upper = (isupper(c[0]) || isupper(c[1]))? 1 : 0;
else if (is_mask) is_upper = (isupper(c[0]) || isupper(c[1]))? 1 : 0;
else is_upper = (isupper(c[0]) && isupper(c[1]))? 1 : 0;
c[0] = seq_nt16_table[c[0]]; c[1] = seq_nt16_table[c[1]];
if (c[0] == 0) c[0] = 15;
if (c[1] == 0) c[1] = 15;
b[0] = bitcnt_table[c[0]];
b[1] = bitcnt_table[c[1]];
if (is_upper) {
if (b[0] == 1 && b[1] == 1) {
if (c[0] == c[1]) ++cnt[0];
else ++cnt[1];
} else if (b[0] == 1 && b[1] == 2) ++cnt[2];
else if (b[0] == 2 && b[1] == 1) ++cnt[3];
else if (b[0] == 2 && b[1] == 2) ++cnt[4];
}
if (is_haploid && (b[0] > 1 || b[1] > 1)) is_upper = 0;
if (is_intersect) {
c[0] = c[0] & c[1];
if (c[0] == 0) is_upper = 0; // FIXME: is this a bug - c[0] cannot be 0!
} else if (is_mask) {
if (c[0] == 15 || c[1] == 15) is_upper = 0;
c[0] &= c[1];
if (c[0] == 0) is_upper = 0;
} else if (is_randhet) {
if (b[0] == 1 && b[1] == 1) { // two homs
c[0] |= c[1];
} else if (((b[0] == 1 && b[1] == 2) || (b[0] == 2 && b[1] == 1)) && (c[0]&c[1])) { // one hom, one het
c[0] = (lrand48()&1)? (c[0] & c[1]) : (c[0] | c[1]);
} else if (b[0] == 2 && b[1] == 2 && c[0] == c[1]) { // double hets
if (lrand48()&1) {
if (lrand48()&1) {
for (i = 8; i >= 1; i >>= 1) // pick the "larger" allele
if (c[0]&i) c[0] &= i;
} else {
for (i = 1; i <= 8; i <<= 1) // pick the "smaller" allele
if (c[0]&i) c[0] &= i;
}
} // else set as het
} else is_upper = 0;
} else c[0] |= c[1];
c[0] = seq_nt16_rev_table[c[0]];
if (!is_upper) c[0] = tolower(c[0]);
if (l%60 == 0) putchar('\n');
putchar(c[0]);
}
putchar('\n');
}
fprintf(stderr, "[%s] (same,diff,hom-het,het-hom,het-het)=(%ld,%ld,%ld,%ld,%ld)\n", __func__, (long)cnt[0], (long)cnt[1], (long)cnt[2], (long)cnt[3], (long)cnt[4]);
return 0;
}
int stk_famask(int argc, char *argv[])
{
gzFile fp[2];
kseq_t *seq[2];
int i, l, c;
while ((c = getopt(argc, argv, "")) >= 0);
if (argc - optind < 2) {
fprintf(stderr, "Usage: seqtk famask <src.fa> <mask.fa>\n");
return 1;
}
for (i = 0; i < 2; ++i) {
fp[i] = strcmp(argv[optind+i], "-")? gzopen(argv[optind+i], "r") : gzdopen(fileno(stdin), "r");
seq[i] = kseq_init(fp[i]);
}
if (fp[0] == 0 || fp[1] == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
while (kseq_read(seq[0]) >= 0) {
int min_l, c[2];
kseq_read(seq[1]);
if (strcmp(seq[0]->name.s, seq[1]->name.s))
fprintf(stderr, "[%s] Different sequence names: %s != %s\n", __func__, seq[0]->name.s, seq[1]->name.s);
if (seq[0]->seq.l != seq[1]->seq.l)
fprintf(stderr, "[%s] Unequal sequence length: %ld != %ld\n", __func__, seq[0]->seq.l, seq[1]->seq.l);
min_l = seq[0]->seq.l < seq[1]->seq.l? seq[0]->seq.l : seq[1]->seq.l;
printf(">%s", seq[0]->name.s);
for (l = 0; l < min_l; ++l) {
c[0] = seq[0]->seq.s[l]; c[1] = seq[1]->seq.s[l];
if (c[1] == 'x') c[0] = tolower(c[0]);
else if (c[1] != 'X') c[0] = c[1];
if (l%60 == 0) putchar('\n');
putchar(c[0]);
}
putchar('\n');
}
return 0;
}
int stk_mutfa(int argc, char *argv[])
{
khash_t(reg) *h = kh_init(reg);
gzFile fp;
kseq_t *seq;
kstream_t *ks;
int l, i, dret;
kstring_t *str;
khint_t k;
if (argc < 3) {
fprintf(stderr, "Usage: seqtk mutfa <in.fa> <in.snp>\n\n");
fprintf(stderr, "Note: <in.snp> contains at least four columns per line which are:\n");
fprintf(stderr, " 'chr 1-based-pos any base-changed-to'.\n");
return 1;
}
// read the list
str = calloc(1, sizeof(kstring_t));
fp = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
ks = ks_init(fp);
while (ks_getuntil(ks, 0, str, &dret) >= 0) {
char *s = strdup(str->s);
int beg = 0, ret;
reglist_t *p;
k = kh_get(reg, h, s);
if (k == kh_end(h)) {
k = kh_put(reg, h, s, &ret);
memset(&kh_val(h, k), 0, sizeof(reglist_t));
}
p = &kh_val(h, k);
if (ks_getuntil(ks, 0, str, &dret) > 0) beg = atol(str->s) - 1; // 2nd col
ks_getuntil(ks, 0, str, &dret); // 3rd col
ks_getuntil(ks, 0, str, &dret); // 4th col
// skip the rest of the line
if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
if (isalpha(str->s[0]) && str->l == 1) {
if (p->n == p->m) {
p->m = p->m? p->m<<1 : 4;
p->a = realloc(p->a, p->m * 8);
}
p->a[p->n++] = (uint64_t)beg<<32 | str->s[0];
}
}
ks_destroy(ks);
gzclose(fp);
free(str->s); free(str);
// mutfa
fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
reglist_t *p;
k = kh_get(reg, h, seq->name.s);
if (k != kh_end(h)) {
p = &kh_val(h, k);
for (i = 0; i < p->n; ++i) {
int beg = p->a[i]>>32;
if (beg < seq->seq.l)
seq->seq.s[beg] = (int)p->a[i];
}
}
printf(">%s", seq->name.s);
for (i = 0; i < l; ++i) {
if (i%60 == 0) putchar('\n');
putchar(seq->seq.s[i]);
}
putchar('\n');
}
// free
kseq_destroy(seq);
gzclose(fp);
for (k = 0; k < kh_end(h); ++k) {
if (kh_exist(h, k)) {
free(kh_val(h, k).a);
free((char*)kh_key(h, k));
}
}
kh_destroy(reg, h);
return 0;
}
int stk_listhet(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq;
int i, l;
if (argc == 1) {
fprintf(stderr, "Usage: seqtk listhet <in.fa>\n");
return 1;
}
fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
for (i = 0; i < l; ++i) {
int b = seq->seq.s[i];
if (bitcnt_table[seq_nt16_table[b]] == 2)
printf("%s\t%d\t%c\n", seq->name.s, i+1, b);
}
}
kseq_destroy(seq);
gzclose(fp);
return 0;
}
/* cutN */
static int cutN_min_N_tract = 1000;
static int cutN_nonN_penalty = 10;
static int find_next_cut(const kseq_t *ks, int k, int *begin, int *end)
{
int i, b, e;
while (k < ks->seq.l) {
if (seq_nt16_table[(int)ks->seq.s[k]] == 15) {
int score, max;
score = 0; e = max = -1;
for (i = k; i < ks->seq.l && score >= 0; ++i) { /* forward */
if (seq_nt16_table[(int)ks->seq.s[i]] == 15) ++score;
else score -= cutN_nonN_penalty;
if (score > max) max = score, e = i;
}
score = 0; b = max = -1;
for (i = e; i >= 0 && score >= 0; --i) { /* backward */
if (seq_nt16_table[(int)ks->seq.s[i]] == 15) ++score;
else score -= cutN_nonN_penalty;
if (score > max) max = score, b = i;
}
if (e + 1 - b >= cutN_min_N_tract) {
*begin = b;
*end = e + 1;
return *end;
}
k = e + 1;
} else ++k;
}
return -1;
}
static void print_seq(FILE *fpout, const kseq_t *ks, int begin, int end)
{
int i;
if (begin >= end) return; // FIXME: why may this happen? Understand it!
fprintf(fpout, "%c%s:%d-%d", ks->qual.l? '@' : '>', ks->name.s, begin+1, end);
for (i = begin; i < end && i < ks->seq.l; ++i) {
if ((i - begin)%60 == 0) fputc('\n', fpout);
fputc(ks->seq.s[i], fpout);
}
fputc('\n', fpout);
if (ks->qual.l == 0) return;
fputs("+\n", fpout);
for (i = begin; i < end && i < ks->qual.l; ++i) {
if ((i - begin)%60 == 0) fputc('\n', fpout);
fputc(ks->qual.s[i], fpout);
}
fputc('\n', fpout);
}
int stk_cutN(int argc, char *argv[])
{
int c, l, gap_only = 0;
gzFile fp;
kseq_t *ks;
while ((c = getopt(argc, argv, "n:p:g")) >= 0) {
switch (c) {
case 'n': cutN_min_N_tract = atoi(optarg); break;
case 'p': cutN_nonN_penalty = atoi(optarg); break;
case 'g': gap_only = 1; break;
default: return 1;
}
}
if (argc == optind) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk cutN [options] <in.fa>\n\n");
fprintf(stderr, "Options: -n INT min size of N tract [%d]\n", cutN_min_N_tract);
fprintf(stderr, " -p INT penalty for a non-N [%d]\n", cutN_nonN_penalty);
fprintf(stderr, " -g print gaps only, no sequence\n\n");
return 1;
}
fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
ks = kseq_init(fp);
while ((l = kseq_read(ks)) >= 0) {
int k = 0, begin = 0, end = 0;
while (find_next_cut(ks, k, &begin, &end) >= 0) {
if (begin != 0) {
if (gap_only) printf("%s\t%d\t%d\n", ks->name.s, begin, end);
else print_seq(stdout, ks, k, begin);
}
k = end;
}
if (!gap_only) print_seq(stdout, ks, k, l);
}
kseq_destroy(ks);
gzclose(fp);
return 0;
}
int stk_hrun(int argc, char *argv[])
{
gzFile fp;
kseq_t *ks;
int min_len = 7, l = 0, c = 0, beg = 0, i;
if (argc == optind) {
fprintf(stderr, "Usage: seqtk hrun <in.fa> [minLen=%d]\n", min_len);
return 1;
}
if (argc == optind + 2) min_len = atoi(argv[optind+1]);
fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
ks = kseq_init(fp);
while (kseq_read(ks) >= 0) {
c = ks->seq.s[0]; l = 1; beg = 0;
for (i = 1; i < ks->seq.l; ++i) {
if (ks->seq.s[i] != c) {
if (l >= min_len) printf("%s\t%d\t%d\t%c\n", ks->name.s, beg, beg + l, c);
c = ks->seq.s[i]; l = 1; beg = i;
} else ++l;
}
}
if (l >= min_len) printf("%s\t%d\t%d\t%c\n", ks->name.s, beg, beg + l, c);
kseq_destroy(ks);
gzclose(fp);
return 0;