Skip to content

Add prefixsplit function #168

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

Add prefixsplit function #168

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
51ffc76
Add prefixsplit function
Feb 22, 2021
2950ce1
fix usage help message
Feb 22, 2021
77fcebc
Add option to only print the sequence with no other information
Feb 23, 2021
0eee545
add seqtk exe to gitignore
Feb 23, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,3 +2,5 @@
*.a
*.dSYM
.*.swp

seqtk
188 changes: 169 additions & 19 deletions seqtk.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -246,6 +246,21 @@ static void stk_printstr(FILE *fp, const kstring_t *s, unsigned line_len)
}
}

static void stk_printstr_compact(FILE *fp, 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) {
fputc('\n', fp);
if (rest > line_len) fwrite(s->s + i, 1, line_len, fp);
else fwrite(s->s + i, 1, rest, fp);
}
} else {
fputc('\n', fp);
fputs(s->s, fp);
}
}

static inline void stk_printseq_renamed(FILE *fp, const kseq_t *s, int line_len, const char *prefix, int64_t n)
{
fputc(s->qual.l? '@' : '>', fp);
Expand Down Expand Up @@ -1890,31 +1905,165 @@ int stk_fqchk(int argc, char *argv[])
return 0;
}


int compare(const void *a, const void *b)
{
return strcmp(*(char**)a, *(char**)b);
}

int prefixsplit(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq;
int c, i, flag = 0, l = UINT_MAX, p = 0, n = 1;
char *prefix, *fn, *pseq;
FILE **out;

while ((c = getopt(argc, argv, "p:ACS")) >= 0) {
switch (c) {
case 'A': flag |= 1; break;
case 'C': flag |= 2; break;
case 'S': flag |= 4; break;
case 'p': p = atoi(optarg); break;
}
}

if (argc == optind) {
fprintf(stderr, "Usage: seqtk prefixsplit [options] <filename> <in.fa>\n");
fprintf(stderr, "Options:\n");
fprintf(stderr, " -p INT length of prefix [%d]\n", n);
fprintf(stderr, " -A force FASTA output (discard quality)\n");
fprintf(stderr, " -C drop comments at the header lines\n");
fprintf(stderr, " -S drop read ID, i.e. only print sequence (overrides A and C options) \n");
return 1;
}

prefix = argv[optind];
fp = (strcmp(argv[optind+1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind+1], "r");

if (fp == 0) {
fprintf(stderr, "[E::%s] failed to open the input file/stream.\n", __func__);
return 1;
}

n = pow(4, p);

char* m[n];

char* m_1[] = {"A", "C", "G", "T"};
char* m_2[] = {"AA", "AC", "AG", "AT", "CA", "CC", "CG", "CT", "GA", "GC", "GG", "GT", "TA", "TC", "TG", "TT"};
char* m_3[] = {"AAA", "AAC", "AAG", "AAT", "ACA", "ACC", "ACG", "ACT", "AGA", "AGC", "AGG", "AGT", "ATA", "ATC", "ATG", "ATT",
"CAA", "CAC", "CAG", "CAT", "CCA", "CCC", "CCG", "CCT", "CGA", "CGC", "CGG", "CGT", "CTA", "CTC", "CTG", "CTT",
"GAA", "GAC", "GAG", "GAT", "GCA", "GCC", "GCG", "GCT", "GGA", "GGC", "GGG", "GGT", "GTA", "GTC", "GTG", "GTT",
"TAA", "TAC", "TAG", "TAT", "TCA", "TCC", "TCG", "TCT", "TGA", "TGC", "TGG", "TGT", "TTA", "TTC", "TTG", "TTT"};

if (p == 1) {
for( i = 0; i < n; i++ ) {
m[i] = m_1[i];
}
} else if (p == 2) {
for( i = 0; i < n; i++ ) {
m[i] = m_2[i];
}
} else if (p == 3) {
for( i = 0; i < n; i++ ) {
m[i] = m_3[i];
}
} else {
fprintf(stderr, "couldnt determined prefix array \n");
return 1;
}

out = (FILE**)malloc(sizeof(FILE*) * (n+1));

fn = (char*)malloc(strlen(prefix) + 10);

/*create n files */
for (i = 0; i < n; ++i) {
if (flag & 1){
sprintf(fn, "%s.%s.fa", prefix, m[i]);
} else {
sprintf(fn, "%s.%s.fastq", prefix, m[i]);
}


out[i] = fopen(fn, "w+");
if (out[i] == 0) {
fprintf(stderr, "ERROR: failed to create file %s\n", fn);
exit(1);
}
}

/*open an extra files for prefixes with an N in them */
if (flag & 1){
sprintf(fn, "%s.N.fa", prefix);
} else {
sprintf(fn, "%s.N.fastq", prefix);
}
out[n] = fopen(fn, "w+");

free(fn);
seq = kseq_init(fp);
size_t mlen = sizeof(m)/sizeof(m[0]);
pseq = malloc(p);
i = 0;

while ((kseq_read(seq)) >= 0) {
memcpy( pseq, &seq->seq.s[0], p );
if (flag & 1) seq->qual.l = 0; // option -a: fastq -> fasta
if (flag & 2) seq->comment.l = 0; // option -C: drop fasta/q comments
char** q = bsearch(&pseq, m, mlen, sizeof(m[0]), compare);
if ( q != NULL )
{
int pos=q-m;
if (flag & 4){
stk_printstr_compact(out[pos], &seq->seq, l);
} else {
stk_printseq(out[pos], seq, l);
}
} else {
if (flag & 4){
stk_printstr_compact(out[n], &seq->seq, l);
} else {
stk_printseq(out[n], seq, l);
}
}
i++;
}

for (i = 0; i <= n; ++i) fclose(out[i]);
free(out);
kseq_destroy(seq);
gzclose(fp);
return 0;
}

/* main function */
static int usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Usage: seqtk <command> <arguments>\n");
fprintf(stderr, "Version: 1.3-r116-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, " gap get the gap locations\n");
fprintf(stderr, " listhet extract the position of each het\n");
fprintf(stderr, " hpc homopolyer-compressed sequence\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, " gap get the gap locations\n");
fprintf(stderr, " listhet extract the position of each het\n");
fprintf(stderr, " hpc homopolyer-compressed sequence\n");
fprintf(stderr, " prefixsplit split FASTA/Q based on read prefix\n");
fprintf(stderr, "\n");
return 1;
}
Expand Down Expand Up @@ -1944,6 +2093,7 @@ int main(int argc, char *argv[])
else if (strcmp(argv[1], "rename") == 0) return stk_rename(argc-1, argv+1);
else if (strcmp(argv[1], "split") == 0) return stk_split(argc-1, argv+1);
else if (strcmp(argv[1], "hpc") == 0) return stk_hpc(argc-1, argv+1);
else if (strcmp(argv[1], "prefixsplit") == 0) return prefixsplit(argc-1, argv+1);
else {
fprintf(stderr, "[main] unrecognized command '%s'. Abort!\n", argv[1]);
return 1;
Expand Down