pax_global_header00006660000000000000000000000064121666171000014512gustar00rootroot0000000000000052 comment=2f0d11c015612ac0e31d6dc194df280f19224096 seqtk-1.0/000077500000000000000000000000001216661710000125015ustar00rootroot00000000000000seqtk-1.0/.gitignore000066400000000000000000000000261216661710000144670ustar00rootroot00000000000000*.o *.a *.dSYM .*.swp seqtk-1.0/Makefile000066400000000000000000000002521216661710000141400ustar00rootroot00000000000000CC=gcc CFLAGS=-g -Wall -O2 seqtk:seqtk.c khash.h kseq.h $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm clean: rm -fr gmon.out *.o ext/*.o a.out seqtk *~ *.a *.dSYM session* seqtk-1.0/README.md000066400000000000000000000030221216661710000137550ustar00rootroot00000000000000Introduction ------------ Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Examples -------- * Convert FASTQ to FASTA: seqtk seq -a in.fq.gz > out.fa * Convert ILLUMINA 1.3+ FASTQ to FASTA and mask bases with quality lower than 20 to lowercases (the 1st command line) or to `N` (the 2nd): seqtk seq -aQ64 -q20 in.fq > out.fa seqtk seq -aQ64 -q20 -n N in.fq > out.fa * Fold long FASTA/Q lines and remove FASTA/Q comments: seqtk seq -Cl60 in.fa > out.fa * Convert multi-line FASTQ to 4-line FASTQ: seqtk seq -l0 in.fq > out.fq * Reverse complement FASTA/Q: seqtk seq -r in.fq > out.fq * Extract sequences with names in file `name.lst`, one sequence name per line: seqtk subseq in.fq name.lst > out.fq * Extract sequences in regions contained in file `reg.bed`: seqtk subseq in.fa reg.bed > out.fa * Mask regions in `reg.bed` to lowercases: seqtk seq -M reg.bed in.fa > out.fa * Subsample 10000 read pairs from two large paired FASTQ files (remember to use the same random seed to keep pairing): seqtk sample -s100 read1.fq 10000 > sub1.fq seqtk sample -s100 read2.fq 10000 > sub2.fq * Trim low-quality bases from both ends using the Phred algorithm: seqtk trimfq in.fq > out.fq * Trim 5bp from the left end of each read and 10bp from the right end: seqtk trimfq -b 5 -e 10 in.fa > out.fa seqtk-1.0/khash.h000066400000000000000000000445401216661710000137570ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008, 2009, 2011 by Attractive Chaos 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. */ /* An example: #include "khash.h" KHASH_MAP_INIT_INT(32, char) int main() { int ret, is_missing; khiter_t k; khash_t(32) *h = kh_init(32); k = kh_put(32, h, 5, &ret); kh_value(h, k) = 10; k = kh_get(32, h, 10); is_missing = (k == kh_end(h)); k = kh_get(32, h, 5); kh_del(32, h, k); for (k = kh_begin(h); k != kh_end(h); ++k) if (kh_exist(h, k)) kh_value(h, k) = 1; kh_destroy(32, h); return 0; } */ /* 2011-12-29 (0.2.7): * Minor code clean up; no actual effect. 2011-09-16 (0.2.6): * The capacity is a power of 2. This seems to dramatically improve the speed for simple keys. Thank Zilong Tan for the suggestion. Reference: - http://code.google.com/p/ulib/ - http://nothings.org/computer/judy/ * Allow to optionally use linear probing which usually has better performance for random input. Double hashing is still the default as it is more robust to certain non-random input. * Added Wang's integer hash function (not used by default). This hash function is more robust to certain non-random input. 2011-02-14 (0.2.5): * Allow to declare global functions. 2009-09-26 (0.2.4): * Improve portability 2008-09-19 (0.2.3): * Corrected the example * Improved interfaces 2008-09-11 (0.2.2): * Improved speed a little in kh_put() 2008-09-10 (0.2.1): * Added kh_clear() * Fixed a compiling error 2008-09-02 (0.2.0): * Changed to token concatenation which increases flexibility. 2008-08-31 (0.1.2): * Fixed a bug in kh_get(), which has not been tested previously. 2008-08-31 (0.1.1): * Added destructor */ #ifndef __AC_KHASH_H #define __AC_KHASH_H /*! @header Generic hash table library. */ #define AC_VERSION_KHASH_H "0.2.6" #include #include #include /* compipler specific configuration */ #if UINT_MAX == 0xffffffffu typedef unsigned int khint32_t; #elif ULONG_MAX == 0xffffffffu typedef unsigned long khint32_t; #endif #if ULONG_MAX == ULLONG_MAX typedef unsigned long khint64_t; #else typedef unsigned long long khint64_t; #endif #ifdef _MSC_VER #define inline __inline #endif typedef khint32_t khint_t; typedef khint_t khiter_t; #define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2) #define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1) #define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3) #define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1))) #define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1))) #define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1))) #define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1)) #ifdef KHASH_LINEAR #define __ac_inc(k, m) 1 #else #define __ac_inc(k, m) (((k)>>3 ^ (k)<<3) | 1) & (m) #endif #define __ac_fsize(m) ((m) < 16? 1 : (m)>>4) #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif static const double __ac_HASH_UPPER = 0.77; #define __KHASH_TYPE(name, khkey_t, khval_t) \ typedef struct { \ khint_t n_buckets, size, n_occupied, upper_bound; \ khint32_t *flags; \ khkey_t *keys; \ khval_t *vals; \ } kh_##name##_t; #define KHASH_DECLARE(name, khkey_t, khval_t) \ __KHASH_TYPE(name, khkey_t, khval_t) \ extern kh_##name##_t *kh_init_##name(); \ extern void kh_destroy_##name(kh_##name##_t *h); \ extern void kh_clear_##name(kh_##name##_t *h); \ extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); \ extern void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \ extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \ extern void kh_del_##name(kh_##name##_t *h, khint_t x); #define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ __KHASH_TYPE(name, khkey_t, khval_t) \ SCOPE kh_##name##_t *kh_init_##name() { \ return (kh_##name##_t*)calloc(1, sizeof(kh_##name##_t)); \ } \ SCOPE void kh_destroy_##name(kh_##name##_t *h) \ { \ if (h) { \ free(h->keys); free(h->flags); \ free(h->vals); \ free(h); \ } \ } \ SCOPE void kh_clear_##name(kh_##name##_t *h) \ { \ if (h && h->flags) { \ memset(h->flags, 0xaa, __ac_fsize(h->n_buckets) * sizeof(khint32_t)); \ h->size = h->n_occupied = 0; \ } \ } \ SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ { \ if (h->n_buckets) { \ khint_t inc, k, i, last, mask; \ mask = h->n_buckets - 1; \ k = __hash_func(key); i = k & mask; \ inc = __ac_inc(k, mask); last = i; /* inc==1 for linear probing */ \ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ i = (i + inc) & mask; \ if (i == last) return h->n_buckets; \ } \ return __ac_iseither(h->flags, i)? h->n_buckets : i; \ } else return 0; \ } \ SCOPE void kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \ { /* This function uses 0.25*n_bucktes bytes of working space instead of [sizeof(key_t+val_t)+.25]*n_buckets. */ \ khint32_t *new_flags = 0; \ khint_t j = 1; \ { \ kroundup32(new_n_buckets); \ if (new_n_buckets < 4) new_n_buckets = 4; \ if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0; /* requested size is too small */ \ else { /* hash table size to be changed (shrink or expand); rehash */ \ new_flags = (khint32_t*)malloc(__ac_fsize(new_n_buckets) * sizeof(khint32_t)); \ memset(new_flags, 0xaa, __ac_fsize(new_n_buckets) * sizeof(khint32_t)); \ if (h->n_buckets < new_n_buckets) { /* expand */ \ h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \ if (kh_is_map) h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \ } /* otherwise shrink */ \ } \ } \ if (j) { /* rehashing is needed */ \ for (j = 0; j != h->n_buckets; ++j) { \ if (__ac_iseither(h->flags, j) == 0) { \ khkey_t key = h->keys[j]; \ khval_t val; \ khint_t new_mask; \ new_mask = new_n_buckets - 1; \ if (kh_is_map) val = h->vals[j]; \ __ac_set_isdel_true(h->flags, j); \ while (1) { /* kick-out process; sort of like in Cuckoo hashing */ \ khint_t inc, k, i; \ k = __hash_func(key); \ i = k & new_mask; \ inc = __ac_inc(k, new_mask); \ while (!__ac_isempty(new_flags, i)) i = (i + inc) & new_mask; \ __ac_set_isempty_false(new_flags, i); \ if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { /* kick out the existing element */ \ { khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \ if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \ __ac_set_isdel_true(h->flags, i); /* mark it as deleted in the old hash table */ \ } else { /* write the element and jump out of the loop */ \ h->keys[i] = key; \ if (kh_is_map) h->vals[i] = val; \ break; \ } \ } \ } \ } \ if (h->n_buckets > new_n_buckets) { /* shrink the hash table */ \ h->keys = (khkey_t*)realloc(h->keys, new_n_buckets * sizeof(khkey_t)); \ if (kh_is_map) h->vals = (khval_t*)realloc(h->vals, new_n_buckets * sizeof(khval_t)); \ } \ free(h->flags); /* free the working space */ \ h->flags = new_flags; \ h->n_buckets = new_n_buckets; \ h->n_occupied = h->size; \ h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \ } \ } \ SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ { \ khint_t x; \ if (h->n_occupied >= h->upper_bound) { /* update the hash table */ \ if (h->n_buckets > (h->size<<1)) kh_resize_##name(h, h->n_buckets - 1); /* clear "deleted" elements */ \ else kh_resize_##name(h, h->n_buckets + 1); /* expand the hash table */ \ } /* TODO: to implement automatically shrinking; resize() already support shrinking */ \ { \ khint_t inc, k, i, site, last, mask = h->n_buckets - 1; \ x = site = h->n_buckets; k = __hash_func(key); i = k & mask; \ if (__ac_isempty(h->flags, i)) x = i; /* for speed up */ \ else { \ inc = __ac_inc(k, mask); last = i; \ while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \ if (__ac_isdel(h->flags, i)) site = i; \ i = (i + inc) & mask; \ if (i == last) { x = site; break; } \ } \ if (x == h->n_buckets) { \ if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \ else x = i; \ } \ } \ } \ if (__ac_isempty(h->flags, x)) { /* not present at all */ \ h->keys[x] = key; \ __ac_set_isboth_false(h->flags, x); \ ++h->size; ++h->n_occupied; \ *ret = 1; \ } else if (__ac_isdel(h->flags, x)) { /* deleted */ \ h->keys[x] = key; \ __ac_set_isboth_false(h->flags, x); \ ++h->size; \ *ret = 2; \ } else *ret = 0; /* Don't touch h->keys[x] if present and not deleted */ \ return x; \ } \ SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ { \ if (x != h->n_buckets && !__ac_iseither(h->flags, x)) { \ __ac_set_isdel_true(h->flags, x); \ --h->size; \ } \ } #define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \ KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) /* --- BEGIN OF HASH FUNCTIONS --- */ /*! @function @abstract Integer hash function @param key The integer [khint32_t] @return The hash value [khint_t] */ #define kh_int_hash_func(key) (khint32_t)(key) /*! @function @abstract Integer comparison function */ #define kh_int_hash_equal(a, b) ((a) == (b)) /*! @function @abstract 64-bit integer hash function @param key The integer [khint64_t] @return The hash value [khint_t] */ #define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11) /*! @function @abstract 64-bit integer comparison function */ #define kh_int64_hash_equal(a, b) ((a) == (b)) /*! @function @abstract const char* hash function @param s Pointer to a null terminated string @return The hash value */ static inline khint_t __ac_X31_hash_string(const char *s) { khint_t h = *s; if (h) for (++s ; *s; ++s) h = (h << 5) - h + *s; return h; } /*! @function @abstract Another interface to const char* hash function @param key Pointer to a null terminated string [const char*] @return The hash value [khint_t] */ #define kh_str_hash_func(key) __ac_X31_hash_string(key) /*! @function @abstract Const char* comparison function */ #define kh_str_hash_equal(a, b) (strcmp(a, b) == 0) static inline khint_t __ac_Wang_hash(khint_t key) { key += ~(key << 15); key ^= (key >> 10); key += (key << 3); key ^= (key >> 6); key += ~(key << 11); key ^= (key >> 16); return key; } #define kh_int_hash_func2(k) __ac_Wang_hash((khint_t)key) /* --- END OF HASH FUNCTIONS --- */ /* Other convenient macros... */ /*! @abstract Type of the hash table. @param name Name of the hash table [symbol] */ #define khash_t(name) kh_##name##_t /*! @function @abstract Initiate a hash table. @param name Name of the hash table [symbol] @return Pointer to the hash table [khash_t(name)*] */ #define kh_init(name) kh_init_##name() /*! @function @abstract Destroy a hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] */ #define kh_destroy(name, h) kh_destroy_##name(h) /*! @function @abstract Reset a hash table without deallocating memory. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] */ #define kh_clear(name, h) kh_clear_##name(h) /*! @function @abstract Resize a hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param s New size [khint_t] */ #define kh_resize(name, h, s) kh_resize_##name(h, s) /*! @function @abstract Insert a key to the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Key [type of keys] @param r Extra return code: 0 if the key is present in the hash table; 1 if the bucket is empty (never used); 2 if the element in the bucket has been deleted [int*] @return Iterator to the inserted element [khint_t] */ #define kh_put(name, h, k, r) kh_put_##name(h, k, r) /*! @function @abstract Retrieve a key from the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Key [type of keys] @return Iterator to the found element, or kh_end(h) is the element is absent [khint_t] */ #define kh_get(name, h, k) kh_get_##name(h, k) /*! @function @abstract Remove a key from the hash table. @param name Name of the hash table [symbol] @param h Pointer to the hash table [khash_t(name)*] @param k Iterator to the element to be deleted [khint_t] */ #define kh_del(name, h, k) kh_del_##name(h, k) /*! @function @abstract Test whether a bucket contains data. @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return 1 if containing data; 0 otherwise [int] */ #define kh_exist(h, x) (!__ac_iseither((h)->flags, (x))) /*! @function @abstract Get key given an iterator @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return Key [type of keys] */ #define kh_key(h, x) ((h)->keys[x]) /*! @function @abstract Get value given an iterator @param h Pointer to the hash table [khash_t(name)*] @param x Iterator to the bucket [khint_t] @return Value [type of values] @discussion For hash sets, calling this results in segfault. */ #define kh_val(h, x) ((h)->vals[x]) /*! @function @abstract Alias of kh_val() */ #define kh_value(h, x) ((h)->vals[x]) /*! @function @abstract Get the start iterator @param h Pointer to the hash table [khash_t(name)*] @return The start iterator [khint_t] */ #define kh_begin(h) (khint_t)(0) /*! @function @abstract Get the end iterator @param h Pointer to the hash table [khash_t(name)*] @return The end iterator [khint_t] */ #define kh_end(h) ((h)->n_buckets) /*! @function @abstract Get the number of elements in the hash table @param h Pointer to the hash table [khash_t(name)*] @return Number of elements in the hash table [khint_t] */ #define kh_size(h) ((h)->size) /*! @function @abstract Get the number of buckets in the hash table @param h Pointer to the hash table [khash_t(name)*] @return Number of buckets in the hash table [khint_t] */ #define kh_n_buckets(h) ((h)->n_buckets) /* More conenient interfaces */ /*! @function @abstract Instantiate a hash set containing integer keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_INT(name) \ KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal) /*! @function @abstract Instantiate a hash map containing integer keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_INT(name, khval_t) \ KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) /*! @function @abstract Instantiate a hash map containing 64-bit integer keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_INT64(name) \ KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) /*! @function @abstract Instantiate a hash map containing 64-bit integer keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_INT64(name, khval_t) \ KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) typedef const char *kh_cstr_t; /*! @function @abstract Instantiate a hash map containing const char* keys @param name Name of the hash table [symbol] */ #define KHASH_SET_INIT_STR(name) \ KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) /*! @function @abstract Instantiate a hash map containing const char* keys @param name Name of the hash table [symbol] @param khval_t Type of values [type] */ #define KHASH_MAP_INIT_STR(name, khval_t) \ KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) #endif /* __AC_KHASH_H */ seqtk-1.0/kseq.h000066400000000000000000000211531216661710000136170ustar00rootroot00000000000000/* The MIT License Copyright (c) 2008, 2009, 2011 Attractive Chaos 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. */ /* Last Modified: 05MAR2012 */ #ifndef AC_KSEQ_H #define AC_KSEQ_H #include #include #include #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r #define KS_SEP_TAB 1 // isspace() && !' ' #define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows) #define KS_SEP_MAX 2 #define __KS_TYPE(type_t) \ typedef struct __kstream_t { \ unsigned char *buf; \ int begin, end, is_eof; \ type_t f; \ } kstream_t; #define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end) #define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0) #define __KS_BASIC(type_t, __bufsize) \ static inline kstream_t *ks_init(type_t f) \ { \ kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \ ks->f = f; \ ks->buf = (unsigned char*)malloc(__bufsize); \ return ks; \ } \ static inline void ks_destroy(kstream_t *ks) \ { \ if (ks) { \ free(ks->buf); \ free(ks); \ } \ } #define __KS_GETC(__read, __bufsize) \ static inline int ks_getc(kstream_t *ks) \ { \ if (ks->is_eof && ks->begin >= ks->end) return -1; \ if (ks->begin >= ks->end) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) return -1; \ } \ return (int)ks->buf[ks->begin++]; \ } #ifndef KSTRING_T #define KSTRING_T kstring_t typedef struct __kstring_t { size_t l, m; char *s; } kstring_t; #endif #ifndef kroundup32 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) #endif #define __KS_GETUNTIL(__read, __bufsize) \ static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \ { \ if (dret) *dret = 0; \ str->l = append? str->l : 0; \ if (ks->begin >= ks->end && ks->is_eof) return -1; \ for (;;) { \ int i; \ if (ks->begin >= ks->end) { \ if (!ks->is_eof) { \ ks->begin = 0; \ ks->end = __read(ks->f, ks->buf, __bufsize); \ if (ks->end < __bufsize) ks->is_eof = 1; \ if (ks->end == 0) break; \ } else break; \ } \ if (delimiter == KS_SEP_LINE) { \ for (i = ks->begin; i < ks->end; ++i) \ if (ks->buf[i] == '\n') break; \ } else if (delimiter > KS_SEP_MAX) { \ for (i = ks->begin; i < ks->end; ++i) \ if (ks->buf[i] == delimiter) break; \ } else if (delimiter == KS_SEP_SPACE) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i])) break; \ } else if (delimiter == KS_SEP_TAB) { \ for (i = ks->begin; i < ks->end; ++i) \ if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \ } else i = 0; /* never come to here! */ \ if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \ str->m = str->l + (i - ks->begin) + 1; \ kroundup32(str->m); \ str->s = (char*)realloc(str->s, str->m); \ } \ memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \ str->l = str->l + (i - ks->begin); \ ks->begin = i + 1; \ if (i < ks->end) { \ if (dret) *dret = ks->buf[i]; \ break; \ } \ } \ if (str->s == 0) { \ str->m = 1; \ str->s = (char*)calloc(1, 1); \ } else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \ str->s[str->l] = '\0'; \ return str->l; \ } \ static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ { return ks_getuntil2(ks, delimiter, str, dret, 0); } #define KSTREAM_INIT(type_t, __read, __bufsize) \ __KS_TYPE(type_t) \ __KS_BASIC(type_t, __bufsize) \ __KS_GETC(__read, __bufsize) \ __KS_GETUNTIL(__read, __bufsize) #define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0) #define __KSEQ_BASIC(SCOPE, type_t) \ SCOPE kseq_t *kseq_init(type_t fd) \ { \ kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \ s->f = ks_init(fd); \ return s; \ } \ SCOPE void kseq_destroy(kseq_t *ks) \ { \ if (!ks) return; \ free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \ ks_destroy(ks->f); \ free(ks); \ } /* Return value: >=0 length of the sequence (normal) -1 end-of-file -2 truncated quality string */ #define __KSEQ_READ(SCOPE) \ SCOPE int kseq_read(kseq_t *seq) \ { \ int c; \ kstream_t *ks = seq->f; \ if (seq->last_char == 0) { /* then jump to the next header line */ \ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \ if (c == -1) return -1; /* end of file */ \ seq->last_char = c; \ } /* else: the first header char has been read in the previous call */ \ seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \ if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \ if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \ if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \ seq->seq.m = 256; \ seq->seq.s = (char*)malloc(seq->seq.m); \ } \ while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \ if (c == '\n') continue; /* skip empty lines */ \ seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \ ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \ } \ if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \ if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \ seq->seq.m = seq->seq.l + 2; \ kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \ seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \ } \ seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \ if (c != '+') return seq->seq.l; /* FASTA */ \ if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \ seq->qual.m = seq->seq.m; \ seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \ } \ while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \ if (c == -1) return -2; /* error: no quality string */ \ while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \ seq->last_char = 0; /* we have not come to the next header line */ \ if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \ return seq->seq.l; \ } #define __KSEQ_TYPE(type_t) \ typedef struct { \ kstring_t name, comment, seq, qual; \ int last_char; \ kstream_t *f; \ } kseq_t; #define KSEQ_INIT2(SCOPE, type_t, __read) \ KSTREAM_INIT(type_t, __read, 16384) \ __KSEQ_TYPE(type_t) \ __KSEQ_BASIC(SCOPE, type_t) \ __KSEQ_READ(SCOPE) #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) #define KSEQ_DECLARE(type_t) \ __KS_TYPE(type_t) \ __KSEQ_TYPE(type_t) \ extern kseq_t *kseq_init(type_t fd); \ void kseq_destroy(kseq_t *ks); \ int kseq_read(kseq_t *seq); #endif seqtk-1.0/seqtk.c000066400000000000000000001024471216661710000140040ustar00rootroot00000000000000/* The MIT License Copyright (c) 20082-2012 by Heng Li 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 #include #include #include #include #include #include #include #include #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) 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 str = calloc(1, sizeof(kstring_t)); fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r"); ks = ks_init(fp); 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 }; 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) { 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); } } void stk_printseq(const kseq_t *s, int line_len) { putchar(s->qual.l? '@' : '>'); 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); } } /* 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; while ((c = getopt(argc, argv, "l:q:b:e:")) >= 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; } } if (optind == argc) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: seqtk trimfq [options] \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, "\n"); return 1; } fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r"); 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) { beg = left; end = seq->seq.l - right; if (beg >= end) beg = end = 0; } 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; } 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->qual.l? '@' : '>'); 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->qual.l) { 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) { fprintf(stderr, "Usage: seqtk comp [-u] [-r in.bed] \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_randbase(int argc, char *argv[]) { gzFile fp; kseq_t *seq; int l; if (argc == 1) { fprintf(stderr, "Usage: seqtk randbase \n"); return 1; } fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r"); 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<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] \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"); 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 = 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] |\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; } /* 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] \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]); } 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; if (argc < 3) { fprintf(stderr, "Usage: seqtk famask \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]); } 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 \n\n"); fprintf(stderr, "Note: 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"); 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"); 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 \n"); return 1; } fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r"); 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, ">%s:%d-%d", 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); } 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] \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"); 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 [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"); 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); } int stk_sample(int argc, char *argv[]) { int c; uint64_t i, num = 0, n_seqs = 0; double frac = 0.; gzFile fp; kseq_t *seq, *buf = 0; srand48(11); while ((c = getopt(argc, argv, "s:")) >= 0) switch (c) { case 's': srand48(atoi(optarg)); break; } if (optind + 2 > argc) { fprintf(stderr, "Usage: seqtk sample [-s seed=11] |\n\n"); fprintf(stderr, "Warning: Large memory consumption for large .\n"); return 1; } frac = atof(argv[optind+1]); if (frac > 1.) num = (uint64_t)(frac + .499), frac = 0.; if (num > 0) buf = calloc(num, sizeof(kseq_t)); fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r"); seq = kseq_init(fp); while (kseq_read(seq) >= 0) { double r = drand48(); ++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); } kseq_destroy(seq); gzclose(fp); 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); } free(buf); 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; unsigned line_len = 0; double frac = 1.; khash_t(reg) *h = 0; srand48(11); while ((c = getopt(argc, argv, "q:l:Q:aACrn:s:f:M:L:c")) >= 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 '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 'l': line_len = atoi(optarg); break; case 'L': min_len = atoi(optarg); break; case 's': srand48(atoi(optarg)); break; case 'f': frac = atof(optarg); break; } } if (argc == optind) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: seqtk seq [options] |\n\n"); fprintf(stderr, "Options: -q INT mask bases with quality lower than INT [0]\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"); return 1; } if (line_len == 0) line_len = UINT_MAX; fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r"); seq = kseq_init(fp); qual_thres += qual_shift; while (kseq_read(seq) >= 0) { if (seq->seq.l < min_len) continue; // NB: length filter before taking random if (frac < 1. && drand48() >= frac) continue; if (seq->qual.l && qual_thres > qual_shift) { unsigned i; if (mask_chr) { for (i = 0; i < seq->seq.l; ++i) if (seq->qual.s[i] < qual_thres) seq->seq.s[i] = mask_chr; } else { for (i = 0; i < seq->seq.l; ++i) if (seq->qual.s[i] < qual_thres) seq->seq.s[i] = tolower(seq->seq.s[i]); } } if (flag & 1) seq->qual.l = 0; if (flag & 2) seq->comment.l = 0; if (h) stk_mask(seq, h, flag&8, mask_chr); // masking if (flag & 4) { // reverse complement int c0, c1; unsigned i; 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; } } stk_printseq(seq, line_len); } kseq_destroy(seq); gzclose(fp); stk_reg_destroy(h); return 0; } /* main function */ static int usage() { fprintf(stderr, "\n"); fprintf(stderr, "Usage: seqtk \n"); fprintf(stderr, "Version: 1.0-r31\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, " trimfq trim FASTQ using the Phred algorithm\n\n"); fprintf(stderr, " hety regional heterozygosity\n"); fprintf(stderr, " mutfa point mutate FASTA at specified positions\n"); fprintf(stderr, " mergefa merge two FASTA/Q files\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], "hety") == 0) stk_hety(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], "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 { fprintf(stderr, "[main] unrecognized commad '%s'. Abort!\n", argv[1]); return 1; } return 0; }