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32e7903 Feb 11, 2017
@lh3 @vsbuffalo @kdmurray91 @zachcp @bwlang
1717 lines (1627 sloc) 53 KB
/* 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;
}
/* sample */
static void cpy_kstr(kstring_t *dst, const kstring_t *src)
{
if (src->l == 0) return;
if (src->l + 1 > dst->m) {
dst->m = src->l + 1;
kroundup32(dst->m);
dst->s = realloc(dst->s, dst->m);
}
dst->l = src->l;
memcpy(dst->s, src->s, src->l + 1);
}
static void cpy_kseq(kseq_t *dst, const kseq_t *src)
{
cpy_kstr(&dst->name, &src->name);
cpy_kstr(&dst->seq, &src->seq);
cpy_kstr(&dst->qual, &src->qual);
cpy_kstr(&dst->comment, &src->comment);
}
int stk_sample(int argc, char *argv[])
{
int c, twopass = 0;
uint64_t i, num = 0, n_seqs = 0;
double frac = 0.;
gzFile fp;
kseq_t *seq;
krand_t *kr = 0;
while ((c = getopt(argc, argv, "2s:")) >= 0)
if (c == 's') kr = kr_srand(atol(optarg));
else if (c == '2') twopass = 1;
if (optind + 2 > argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk sample [-2] [-s seed=11] <in.fa> <frac>|<number>\n\n");
fprintf(stderr, "Options: -s INT RNG seed [11]\n");
fprintf(stderr, " -2 2-pass mode: twice as slow but with much reduced memory\n\n");
return 1;
}
frac = atof(argv[optind+1]);
if (frac > 1.) num = (uint64_t)(frac + .499), frac = 0.;
else if (twopass) {
fprintf(stderr, "[W::%s] when sampling a fraction, option -2 is ignored.", __func__);
twopass = 0;
}
if (kr == 0) kr = kr_srand(11);
if (!twopass) { // the streaming version
kseq_t *buf = 0;
if (num > 0) buf = calloc(num, sizeof(kseq_t));
if (num > 0 && buf == NULL) {
fprintf(stderr, "[E::%s] Could not allocate enough memory for %" PRIu64 " sequences. Exiting...\n", __func__, num);
free(kr);
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);
n_seqs = 0;
while (kseq_read(seq) >= 0) {
double r = kr_drand(kr);
++n_seqs;
if (num) {
uint64_t y = n_seqs - 1 < num? n_seqs - 1 : (uint64_t)(r * n_seqs);
if (y < num) cpy_kseq(&buf[y], seq);
} else if (r < frac) stk_printseq(seq, UINT_MAX);
}
for (i = 0; i < num; ++i) {
kseq_t *p = &buf[i];
if (p->seq.l) stk_printseq(p, UINT_MAX);
free(p->seq.s); free(p->qual.s); free(p->name.s);
}
if (buf != NULL) free(buf);
} else {
uint64_t *buf;
khash_t(64) *hash;
int absent;
if (strcmp(argv[optind], "-") == 0) {
fprintf(stderr, "[E::%s] in the 2-pass mode, the input cannot be STDIN.\n", __func__);
free(kr);
return 1;
}
// 1st pass
buf = malloc(num * 8);
for (i = 0; i < num; ++i) buf[i] = UINT64_MAX;
fp = 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);
n_seqs = 0;
while (kseq_read(seq) >= 0) {
double r = kr_drand(kr);
uint64_t y;
++n_seqs;
y = n_seqs - 1 < num? n_seqs - 1 : (uint64_t)(r * n_seqs);
if (y < num) buf[y] = n_seqs;
}
kseq_destroy(seq);
gzclose(fp);
hash = kh_init(64);
for (i = 0; i < num; ++i) kh_put(64, hash, buf[i], &absent);
free(buf);
// 2nd pass
fp = gzopen(argv[optind], "r");
seq = kseq_init(fp);
n_seqs = 0;
while (kseq_read(seq) >= 0)
if (kh_get(64, hash, ++n_seqs) != kh_end(hash))
stk_printseq(seq, UINT_MAX);
kh_destroy(64, hash);
}
kseq_destroy(seq);
gzclose(fp);
free(kr);
return 0;
}
/* seq */
void stk_mask(kseq_t *seq, const khash_t(reg) *h, int is_complement, int mask_chr)
{
unsigned i, j;
khiter_t k;
k = kh_get(reg, h, seq->name.s);
if (k == kh_end(h)) { // not found in the hash table
if (is_complement) {
if (mask_chr) {
for (j = 0; j < seq->seq.l; ++j)
seq->seq.s[j] = mask_chr;
} else {
for (j = 0; j < seq->seq.l; ++j)
seq->seq.s[j] = tolower(seq->seq.s[j]);
}
}
} else {
reglist_t *p = &kh_val(h, k);
if (!is_complement) {
for (i = 0; i < p->n; ++i) {
unsigned beg = p->a[i]>>32, end = p->a[i];
if (beg >= seq->seq.l) continue;
if (end > seq->seq.l) end = seq->seq.l;
if (!mask_chr) for (j = beg; j < end; ++j) seq->seq.s[j] = tolower(seq->seq.s[j]);
else for (j = beg; j < end; ++j) seq->seq.s[j] = mask_chr;
}
} else {
int8_t *mask = calloc(seq->seq.l, 1);
for (i = 0; i < p->n; ++i) {
unsigned beg = p->a[i]>>32, end = p->a[i];
if (end >= seq->seq.l) end = seq->seq.l;
for (j = beg; j < end; ++j) mask[j] = 1;
}
if (mask_chr) {
for (j = 0; j < seq->seq.l; ++j)
if (mask[j] == 0) seq->seq.s[j] = mask_chr;
} else {
for (j = 0; j < seq->seq.l; ++j)
if (mask[j] == 0) seq->seq.s[j] = tolower(seq->seq.s[j]);
}
free(mask);
}
}
}
int stk_seq(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq;
int c, qual_thres = 0, flag = 0, qual_shift = 33, mask_chr = 0, min_len = 0, max_q = 255;
unsigned i, line_len = 0;
int64_t n_seqs = 0;
double frac = 1.;
khash_t(reg) *h = 0;
krand_t *kr = 0;
while ((c = getopt(argc, argv, "N12q:l:Q:aACrn:s:f:M:L:cVUX:S")) >= 0) {
switch (c) {
case 'a':
case 'A': flag |= 1; break;
case 'C': flag |= 2; break;
case 'r': flag |= 4; break;
case 'c': flag |= 8; break;
case '1': flag |= 16; break;
case '2': flag |= 32; break;
case 'V': flag |= 64; break;
case 'N': flag |= 128; break;
case 'U': flag |= 256; break;
case 'S': flag |= 512; break;
case 'M': h = stk_reg_read(optarg); break;
case 'n': mask_chr = *optarg; break;
case 'Q': qual_shift = atoi(optarg); break;
case 'q': qual_thres = atoi(optarg); break;
case 'X': max_q = atoi(optarg); break;
case 'l': line_len = atoi(optarg); break;
case 'L': min_len = atoi(optarg); break;
case 's': kr = kr_srand(atol(optarg)); break;
case 'f': frac = atof(optarg); break;
}
}
if (kr == 0) kr = kr_srand(11);
if (argc == optind && isatty(fileno(stdin))) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk seq [options] <in.fq>|<in.fa>\n\n");
fprintf(stderr, "Options: -q INT mask bases with quality lower than INT [0]\n");
fprintf(stderr, " -X INT mask bases with quality higher than INT [255]\n");
fprintf(stderr, " -n CHAR masked bases converted to CHAR; 0 for lowercase [0]\n");
fprintf(stderr, " -l INT number of residues per line; 0 for 2^32-1 [%d]\n", line_len);
fprintf(stderr, " -Q INT quality shift: ASCII-INT gives base quality [%d]\n", qual_shift);
fprintf(stderr, " -s INT random seed (effective with -f) [11]\n");
fprintf(stderr, " -f FLOAT sample FLOAT fraction of sequences [1]\n");
fprintf(stderr, " -M FILE mask regions in BED or name list FILE [null]\n");
fprintf(stderr, " -L INT drop sequences with length shorter than INT [0]\n");
fprintf(stderr, " -c mask complement region (effective with -M)\n");
fprintf(stderr, " -r reverse complement\n");
fprintf(stderr, " -A force FASTA output (discard quality)\n");
fprintf(stderr, " -C drop comments at the header lines\n");
fprintf(stderr, " -N drop sequences containing ambiguous bases\n");
fprintf(stderr, " -1 output the 2n-1 reads only\n");
fprintf(stderr, " -2 output the 2n reads only\n");
fprintf(stderr, " -V shift quality by '(-Q) - 33'\n");
fprintf(stderr, " -U convert all bases to uppercases\n");
fprintf(stderr, " -S strip of white spaces in sequences\n");
fprintf(stderr, "\n");
free(kr);
return 1;
}
if (line_len == 0) line_len = UINT_MAX;
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);
qual_thres += qual_shift;
while (kseq_read(seq) >= 0) {
++n_seqs;
if (seq->seq.l < min_len) continue; // NB: length filter before taking random
if (frac < 1. && kr_drand(kr) >= frac) continue;
if (flag & 48) { // then choose odd/even reads only
if ((flag&16) && (n_seqs&1) == 0) continue;
if ((flag&32) && (n_seqs&1) == 1) continue;
}
if (flag & 512) { // option -S: squeeze out white spaces
int k;
if (seq->qual.l) {
for (i = k = 0; i < seq->seq.l; ++i)
if (!isspace(seq->seq.s[i]))
seq->qual.s[k++] = seq->qual.s[i];
seq->qual.l = k;
}
for (i = k = 0; i < seq->seq.l; ++i)
if (!isspace(seq->seq.s[i]))
seq->seq.s[k++] = seq->seq.s[i];
seq->seq.l = k;
}
if (seq->qual.l && qual_thres > qual_shift) {
if (mask_chr) {
for (i = 0; i < seq->seq.l; ++i)
if (seq->qual.s[i] < qual_thres || seq->qual.s[i] > max_q)
seq->seq.s[i] = mask_chr;
} else {
for (i = 0; i < seq->seq.l; ++i)
if (seq->qual.s[i] < qual_thres || seq->qual.s[i] > max_q)
seq->seq.s[i] = tolower(seq->seq.s[i]);
}
}
if (flag & 256) // option -U: convert to uppercases
for (i = 0; i < seq->seq.l; ++i)
seq->seq.s[i] = toupper(seq->seq.s[i]);
if (flag & 1) seq->qual.l = 0; // option -a: fastq -> fasta
if (flag & 2) seq->comment.l = 0; // option -C: drop fasta/q comments
if (h) stk_mask(seq, h, flag&8, mask_chr); // masking
if (flag & 4) { // option -r: reverse complement
int c0, c1;
for (i = 0; i < seq->seq.l>>1; ++i) { // reverse complement sequence
c0 = comp_tab[(int)seq->seq.s[i]];
c1 = comp_tab[(int)seq->seq.s[seq->seq.l - 1 - i]];
seq->seq.s[i] = c1;
seq->seq.s[seq->seq.l - 1 - i] = c0;
}
if (seq->seq.l & 1) // complement the remaining base
seq->seq.s[seq->seq.l>>1] = comp_tab[(int)seq->seq.s[seq->seq.l>>1]];
if (seq->qual.l) {
for (i = 0; i < seq->seq.l>>1; ++i) // reverse quality
c0 = seq->qual.s[i], seq->qual.s[i] = seq->qual.s[seq->qual.l - 1 - i], seq->qual.s[seq->qual.l - 1 - i] = c0;
}
}
if ((flag & 64) && seq->qual.l && qual_shift != 33)
for (i = 0; i < seq->qual.l; ++i)
seq->qual.s[i] -= qual_shift - 33;
if (flag & 128) { // option -N: drop sequences containing ambiguous bases - Note: this is the last step!
for (i = 0; i < seq->seq.l; ++i)
if (seq_nt16to4_table[seq_nt16_table[(int)seq->seq.s[i]]] > 3) break;
if (i < seq->seq.l) continue;
}
stk_printseq(seq, line_len);
}
kseq_destroy(seq);
gzclose(fp);
stk_reg_destroy(h);
free(kr);
return 0;
}
int stk_gc(int argc, char *argv[])
{
int c, is_at = 0, min_l = 20;
double frac = 0.6f, xdropoff = 10.0f, q;
gzFile fp;
kseq_t *seq;
while ((c = getopt(argc, argv, "wx:f:l:")) >= 0) {
if (c == 'x') xdropoff = atof(optarg);
else if (c == 'w') is_at = 1;
else if (c == 'f') frac = atof(optarg);
else if (c == 'l') min_l = atoi(optarg);
}
if (optind + 1 > argc) {
fprintf(stderr, "Usage: seqtk gc [options] <in.fa>\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -w identify high-AT regions\n");
fprintf(stderr, " -f FLOAT min GC fraction (or AT fraction for -w) [%.2f]\n", frac);
fprintf(stderr, " -l INT min region length to output [%d]\n", min_l);
fprintf(stderr, " -x FLOAT X-dropoff [%.1f]\n", xdropoff);
return 1;
}
q = (1.0f - frac) / frac;
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 (kseq_read(seq) >= 0) {
int i, start = 0, max_i = 0, n_hits = 0, start_hits = 0, max_hits = 0;
double sc = 0., max = 0.;
for (i = 0; i < seq->seq.l; ++i) {
int hit;
c = seq_nt16_table[(int)seq->seq.s[i]];
if (is_at) hit = (c == 1 || c == 8 || c == 9);
else hit = (c == 2 || c == 4 || c == 6);
n_hits += hit;
if (hit) {
if (sc == 0) start = i, start_hits = n_hits;
sc += q;
if (sc > max) max = sc, max_i = i, max_hits = n_hits;
} else if (sc > 0) {
sc += -1.0f;
if (sc < 0 || max - sc > xdropoff) {
if (max_i + 1 - start >= min_l)
printf("%s\t%d\t%d\t%d\n", seq->name.s, start, max_i + 1, max_hits - start_hits + 1);
sc = max = 0;
i = max_i;
}
}
}
if (max > 0. && max_i + 1 - start >= min_l)
printf("%s\t%d\t%d\t%d\n", seq->name.s, start, max_i + 1, max_hits - start_hits + 1);
}
kseq_destroy(seq);
gzclose(fp);
return 0;
}
int stk_mergepe(int argc, char *argv[])
{
gzFile fp1, fp2;
kseq_t *seq[2];
if (argc < 3) {
fprintf(stderr, "Usage: seqtk mergepe <in1.fq> <in2.fq>\n");
return 1;
}
fp1 = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
fp2 = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
if (fp1 == 0 || fp2 == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}
seq[0] = kseq_init(fp1);
seq[1] = kseq_init(fp2);
while (kseq_read(seq[0]) >= 0) {
if (kseq_read(seq[1]) < 0) {
fprintf(stderr, "[W::%s] the 2nd file has fewer records.\n", __func__);
break;
}
stk_printseq(seq[0], 0);
stk_printseq(seq[1], 0);
}
if (kseq_read(seq[1]) >= 0)
fprintf(stderr, "[W::%s] the 1st file has fewer records.\n", __func__);
kseq_destroy(seq[0]); gzclose(fp1);
kseq_destroy(seq[1]); gzclose(fp2);
return 0;
}
int stk_dropse(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq, last;
if (argc == 1 && isatty(fileno(stdin))) {
fprintf(stderr, "Usage: seqtk dropse <in.fq>\n");
return 1;
}
fp = argc > 1 && 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);
memset(&last, 0, sizeof(kseq_t));
while (kseq_read(seq) >= 0) {
if (last.name.l) {
kstring_t *p = &last.name, *q = &seq->name;
int is_diff;
if (p->l == q->l) {
int l = (p->l > 2 && p->s[p->l-2] == '/' && q->s[q->l-2] == '/' && isdigit(p->s[p->l-1]) && isdigit(q->s[q->l-1]))? p->l - 2 : p->l;
is_diff = strncmp(p->s, q->s, l);
} else is_diff = 1;
if (!is_diff) {
stk_printseq(&last, 0);
stk_printseq(seq, 0);
last.name.l = 0;
} else cpy_kseq(&last, seq);
} else cpy_kseq(&last, seq);
}
kseq_destroy(seq);
gzclose(fp);
// free last!
return 0;
}
int stk_rename(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq, last;
char *prefix = 0;
uint64_t n = 1;
if (argc == 1 && isatty(fileno(stdin))) {
fprintf(stderr, "Usage: seqtk rename <in.fq> [prefix]\n");
return 1;
}
fp = argc > 1 && 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);
if (argc > 2) prefix = argv[2];
memset(&last, 0, sizeof(kseq_t));
while (kseq_read(seq) >= 0) {
if (last.name.l) {
kstring_t *p = &last.name, *q = &seq->name;
int is_diff;
if (p->l == q->l) {
int l = (p->l > 2 && p->s[p->l-2] == '/' && q->s[q->l-2] == '/' && isdigit(p->s[p->l-1]) && isdigit(q->s[q->l-1]))? p->l - 2 : p->l;
is_diff = strncmp(p->s, q->s, l);
} else is_diff = 1;
if (!is_diff) {
stk_printseq_renamed(&last, 0, prefix, n);
stk_printseq_renamed(seq, 0, prefix, n);
last.name.l = 0;
++n;
} else {
stk_printseq_renamed(&last, 0, prefix, n);
++n;
cpy_kseq(&last, seq);
}
} else cpy_kseq(&last, seq);
}
if (last.name.l) stk_printseq_renamed(&last, 0, prefix, n);
kseq_destroy(seq);
gzclose(fp);
// free last!
return 0;
}
int stk_kfreq(int argc, char *argv[])
{
gzFile fp;
kseq_t *ks;
int kmer, i, l, mask;
char *nei;
if (argc < 2) {
fprintf(stderr, "Usage: seqtk kfreq <kmer> <in.fa>\n");
return 1;
}
// get the k-mer
l = strlen(argv[1]);
for (i = kmer = 0; i < l; ++i) {
int c = seq_nt6_table[(int)argv[1][i]];
assert(c >= 1 && c <= 4);
kmer = kmer << 2 | (c - 1);
}
mask = (1<<2*l) - 1;
// get the neighbors
nei = calloc(1, 1<<2*l);
for (i = 0; i < l; ++i) {
int j, x;
x = kmer & ~(3 << 2*i);
for (j = 0; j < 4; ++j)
nei[x|j<<2*i] = 1;
}
fp = argc == 2 || strcmp(argv[2], "-") == 0? gzdopen(fileno(stdin), "r") : gzopen(argv[2], "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) {
int k, x[2], cnt[2], cnt_nei[2], which;
x[0] = x[1] = k = cnt[0] = cnt[1] = cnt_nei[0] = cnt_nei[1] = 0;
for (i = 0; i < ks->seq.l; ++i) {
int c = seq_nt6_table[(int)ks->seq.s[i]];
if (c >= 1 && c <= 4) {
x[0] = (x[0] << 2 | (c - 1)) & mask;
x[1] = (x[1] >> 2 | (4 - c) << 2*(l-1));
if (k < l) ++k;
if (k == l) {
if (x[0] == kmer) ++cnt[0];
else if (x[1] == kmer) ++cnt[1];
if (nei[x[0]]) ++cnt_nei[0];
else if (nei[x[1]]) ++cnt_nei[1];
}
} else k = 0;
}
which = cnt_nei[0] > cnt_nei[1]? 0 : 1;
printf("%s\t%ld\t%c\t%d\t%d\n", ks->name.s, ks->seq.l, "+-"[which], cnt_nei[which], cnt[which]);
}
kseq_destroy(ks);
gzclose(fp);
return 0;
}
/* fqchk */
typedef struct {
int64_t q[94], b[5];
} posstat_t;
static void fqc_aux(posstat_t *p, int pos, int64_t allq[94], double perr[94], int qthres)
{
int k;
int64_t sum = 0, qsum = 0, sum_low = 0;
double psum = 0;
if (pos <= 0) printf("ALL");
else printf("%d", pos);
for (k = 0; k <= 4; ++k) sum += p->b[k];
printf("\t%lld", (long long)sum);
for (k = 0; k <= 4; ++k)
printf("\t%.1f", 100. * p->b[k] / sum);
for (k = 0; k <= 93; ++k) {
qsum += p->q[k] * k, psum += p->q[k] * perr[k];
if (k < qthres) sum_low += p->q[k];
}
printf("\t%.1f\t%.1f", (double)qsum/sum, -4.343*log((psum+1e-6)/(sum+1e-6)));
if (qthres <= 0) {
for (k = 0; k <= 93; ++k)
if (allq[k] > 0) printf("\t%.2f", 100. * p->q[k] / sum);
} else printf("\t%.1f\t%.1f", 100. * sum_low / sum, 100. * (sum - sum_low) / sum);
putchar('\n');
}
int stk_fqchk(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq;
int i, c, k, max_len = 0, min_len = 0x7fffffff, max_alloc = 0, offset = 33, n_diffQ = 0, qthres = 20;
int64_t tot_len = 0, n = 0;
double perr[94];
posstat_t all, *pos = 0;
while ((c = getopt(argc, argv, "q:")) >= 0)
if (c == 'q') qthres = atoi(optarg);
if (optind == argc) {
fprintf(stderr, "Usage: seqtk fqchk [-q %d] <in.fq>\n", qthres);
fprintf(stderr, "Note: use -q0 to get the distribution of all quality values\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;
}
seq = kseq_init(fp);
for (k = 0; k <= 93; ++k)
perr[k] = pow(10., -.1 * k);
perr[0] = perr[1] = perr[2] = perr[3] = .5;
while (kseq_read(seq) >= 0) {
if (seq->qual.l == 0) continue;
++n;
tot_len += seq->seq.l;
min_len = min_len < seq->seq.l? min_len : seq->seq.l;
max_len = max_len > seq->seq.l? max_len : seq->seq.l;
if (max_len > max_alloc) {
int old_max = max_alloc;
max_alloc = max_len;
kroundup32(max_alloc);
pos = realloc(pos, max_alloc * sizeof(posstat_t));
memset(&pos[old_max], 0, (max_alloc - old_max) * sizeof(posstat_t));
}
for (i = 0; i < seq->qual.l; ++i) {
int q = seq->qual.s[i] - offset;
int b = seq_nt6_table[(int)seq->seq.s[i]];
b = b? b - 1 : 4;
q = q < 93? q : 93;
++pos[i].q[q];
++pos[i].b[b];
}
}
kseq_destroy(seq);
gzclose(fp);
memset(&all, 0, sizeof(posstat_t));
for (i = 0; i < max_len; ++i) {
for (k = 0; k <= 93; ++k)
all.q[k] += pos[i].q[k];
for (k = 0; k <= 4; ++k)
all.b[k] += pos[i].b[k];
}
for (k = n_diffQ = 0; k <= 93; ++k)
if (all.q[k]) ++n_diffQ;
printf("min_len: %d; max_len: %d; avg_len: %.2f; %d distinct quality values\n", min_len, max_len, (double)tot_len/n, n_diffQ);
printf("POS\t#bases\t%%A\t%%C\t%%G\t%%T\t%%N\tavgQ\terrQ");
if (qthres <= 0) {
for (k = 0; k <= 93; ++k)
if (all.q[k] > 0) printf("\t%%Q%d", k);
} else printf("\t%%low\t%%high");
putchar('\n');
fqc_aux(&all, 0, all.q, perr, qthres);
for (i = 0; i < max_len; ++i)
fqc_aux(&pos[i], i + 1, all.q, perr, qthres);
free(pos);
return 0;
}
/* main function */
static int usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk <command> <arguments>\n");
fprintf(stderr, "Version: 1.2-r101-dirty\n\n");
fprintf(stderr, "Command: seq common transformation of FASTA/Q\n");
fprintf(stderr, " comp get the nucleotide composition of FASTA/Q\n");
fprintf(stderr, " sample subsample sequences\n");
fprintf(stderr, " subseq extract subsequences from FASTA/Q\n");
fprintf(stderr, " fqchk fastq QC (base/quality summary)\n");
fprintf(stderr, " mergepe interleave two PE FASTA/Q files\n");
fprintf(stderr, " trimfq trim FASTQ using the Phred algorithm\n\n");
fprintf(stderr, " hety regional heterozygosity\n");
fprintf(stderr, " gc identify high- or low-GC regions\n");
fprintf(stderr, " mutfa point mutate FASTA at specified positions\n");
fprintf(stderr, " mergefa merge two FASTA/Q files\n");
fprintf(stderr, " famask apply a X-coded FASTA to a source FASTA\n");
fprintf(stderr, " dropse drop unpaired from interleaved PE FASTA/Q\n");
fprintf(stderr, " rename rename sequence names\n");
fprintf(stderr, " randbase choose a random base from hets\n");
fprintf(stderr, " cutN cut sequence at long N\n");
fprintf(stderr, " listhet extract the position of each het\n");
fprintf(stderr, "\n");
return 1;
}
int main(int argc, char *argv[])
{
if (argc == 1) return usage();
if (strcmp(argv[1], "comp") == 0) stk_comp(argc-1, argv+1);
else if (strcmp(argv[1], "fqchk") == 0) stk_fqchk(argc-1, argv+1);
else if (strcmp(argv[1], "hety") == 0) stk_hety(argc-1, argv+1);
else if (strcmp(argv[1], "gc") == 0) stk_gc(argc-1, argv+1);
else if (strcmp(argv[1], "subseq") == 0) stk_subseq(argc-1, argv+1);
else if (strcmp(argv[1], "mutfa") == 0) stk_mutfa(argc-1, argv+1);
else if (strcmp(argv[1], "mergefa") == 0) stk_mergefa(argc-1, argv+1);
else if (strcmp(argv[1], "mergepe") == 0) stk_mergepe(argc-1, argv+1);
else if (strcmp(argv[1], "dropse") == 0) stk_dropse(argc-1, argv+1);
else if (strcmp(argv[1], "randbase") == 0) stk_randbase(argc-1, argv+1);
else if (strcmp(argv[1], "cutN") == 0) stk_cutN(argc-1, argv+1);
else if (strcmp(argv[1], "listhet") == 0) stk_listhet(argc-1, argv+1);
else if (strcmp(argv[1], "famask") == 0) stk_famask(argc-1, argv+1);
else if (strcmp(argv[1], "trimfq") == 0) stk_trimfq(argc-1, argv+1);
else if (strcmp(argv[1], "hrun") == 0) stk_hrun(argc-1, argv+1);
else if (strcmp(argv[1], "sample") == 0) stk_sample(argc-1, argv+1);
else if (strcmp(argv[1], "seq") == 0) stk_seq(argc-1, argv+1);
else if (strcmp(argv[1], "kfreq") == 0) stk_kfreq(argc-1, argv+1);
else if (strcmp(argv[1], "rename") == 0) stk_rename(argc-1, argv+1);
else {
fprintf(stderr, "[main] unrecognized command '%s'. Abort!\n", argv[1]);
return 1;
}
return 0;
}