/* 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) {
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 = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
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_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 = 1024;
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]);
// subseq
fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
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);
}
} 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 % 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 % line == 0) putchar('\n');
putchar(seq->qual.s[j + beg]);
}
putchar('\n');
}
}
// free
kseq_destroy(seq);
gzclose(fp);
stk_reg_destroy(h);
return 0;
}
int stk_maskseq(int argc, char *argv[])
{
khash_t(reg) *h = kh_init(reg);
gzFile fp;
kseq_t *seq;
int l, i, j, c, is_complement = 0, is_lower = 0;
khint_t k;
while ((c = getopt(argc, argv, "cl")) >= 0) {
switch (c) {
case 'c': is_complement = 1; break;
case 'l': is_lower = 1; break;
}
}
if (argc - optind < 2) {
fprintf(pysamerr, "Usage: seqtk maskseq [-cl] <in.fa> <in.bed>\n\n");
fprintf(pysamerr, "Options: -c mask the complement regions\n");
fprintf(pysamerr, " -l soft mask (to lower cases)\n");
return 1;
}
h = stk_reg_read(argv[optind+1]);
// maskseq
fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
k = kh_get(reg, h, seq->name.s);
if (k == kh_end(h)) { // not found in the hash table
if (is_complement) {
for (j = 0; j < l; ++j)
seq->seq.s[j] = is_lower? tolower(seq->seq.s[j]) : 'N';
}
} else {
reglist_t *p = &kh_val(h, k);
if (!is_complement) {
for (i = 0; i < p->n; ++i) {
int beg = p->a[i]>>32, end = p->a[i];
if (beg >= seq->seq.l) {
fprintf(pysamerr, "[maskseq] start position >= the sequence length.\n");
continue;
}
if (end >= seq->seq.l) end = seq->seq.l;
if (is_lower) 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] = 'N';
}
} else {
int8_t *mask = calloc(seq->seq.l, 1);
for (i = 0; i < p->n; ++i) {
int 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;
}
for (j = 0; j < l; ++j)
if (mask[j] == 0) seq->seq.s[j] = is_lower? tolower(seq->seq.s[j]) : 'N';
free(mask);
}
}
printf(">%s", seq->name.s);
for (j = 0; j < seq->seq.l; ++j) {
if (j%60 == 0) putchar('\n');
putchar(seq->seq.s[j]);
}
putchar('\n');
}
