From 1f312a24606b09cf1a41aa79946b1963a242f648 Mon Sep 17 00:00:00 2001 From: Nicholas Noll Date: Thu, 22 Apr 2021 09:00:11 -0700 Subject: feat(libbio): fasta and newick parsing/output --- sys/libbio/fasta.c | 346 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 346 insertions(+) create mode 100644 sys/libbio/fasta.c (limited to 'sys/libbio/fasta.c') diff --git a/sys/libbio/fasta.c b/sys/libbio/fasta.c new file mode 100644 index 0000000..484ebb2 --- /dev/null +++ b/sys/libbio/fasta.c @@ -0,0 +1,346 @@ +#include +#include +#include + +#define INIT_NM_SIZE 128 +#define INIT_SQ_SIZE 4096 + +struct Seqbuf +{ + mem·Allocator heap; + void *h; + + int len, off; + byte *it, b[]; +}; + +static +void +reset(struct Seqbuf *sb) +{ + sb->off = 0; + sb->it = sb->b; +} + +static +error +grow(struct Seqbuf **sb, int min) +{ + struct Seqbuf *old, *new; + vlong newlen; + + old = *sb; + assert((*sb)->len <= (SIZE_MAX - 1) / 2); + newlen = MAX(16, MAX(1 + 2*(*sb)->len, (*sb)->len+min)); + assert(newlen >= (*sb)->len+min); + + if (new = old->heap.alloc(old->h, 1, sizeof(*new)+newlen), !new) { + errorf("memory: could not allocate new buffer"); + return 1; + } + + memcpy(new, old, sizeof(*sb) + (*sb)->len); + new->len = newlen; + new->it = new->b + (old->len); + old->heap.free(old->h, old); + + *sb = new; + return 0; +} + +static +error +put(struct Seqbuf **sb, byte c) +{ + int err; + struct Seqbuf *sq; + + sq = *sb; + if (sq->it < (sq->b + sq->len)) { + *sq->it++ = c; + return 0; + } + + if (err = grow(sb, 1), err) { + errorf("memory fail: could not allocate more buffer"); + sq->heap.free(sq->h, sq); + return 1; + } + + *((*sb)->it++) = c; + return 0; +} + +static +error +push(struct Seqbuf **sb, int n, void *buf) +{ + int d, err; + struct Seqbuf *seq; + + seq = *sb; + if (d = seq->len - (seq->it - seq->b), d < n) { + assert(d > 0); + if (err = grow(sb, n-d), err) { + errorf("memory fail: could not allocate more buffer"); + seq->heap.free(seq->h, seq); + return 1; + } + } + + memcpy((*sb)->it, buf, n); + (*sb)->it += n; + + return 0; +} + +// ----------------------------------------------------------------------- +// sequence data + +struct bio·SeqReader { + byte eof; + io·Reader file; + void *f; + + struct Seqbuf *seq; + + /* read buffer */ + byte *b, *bend; + byte buf[4*4098]; +}; + +static +error +fill(bio·SeqReader *rdr) +{ + int n; + // NOTE: This could lead to an infinite loop. + if (rdr->eof) { + return 0; + } + + n = rdr->file.read(rdr->f, 1, arrlen(rdr->buf), rdr->buf); + if (n < 0) { + errorf("read: no data obtained from reader"); + return 1; + } + rdr->b = rdr->buf; + rdr->bend = rdr->b + n; + if (rdr->eof = n < arrlen(rdr->buf), rdr->eof) { + *rdr->bend++ = '\0'; + } + + return 0; +} + +bio·SeqReader* +bio·openseq(io·Reader file, void *f, mem·Allocator heap, void *h) +{ + error err; + bio·SeqReader *rdr; + + rdr = heap.alloc(h, 1, sizeof(bio·SeqReader)); + rdr->file = file; + rdr->f = f; + rdr->eof = 0; + + rdr->seq = heap.alloc(h, 1, sizeof(*rdr->seq) + INIT_NM_SIZE + INIT_SQ_SIZE); + rdr->seq->heap = heap; + rdr->seq->h = h; + rdr->seq->it = rdr->seq->b; + rdr->seq->len = INIT_NM_SIZE + INIT_SQ_SIZE; + + if (err = fill(rdr), err) { + errorf("fill: could not populate buffer"); + goto ERROR; + } + + return rdr; + +ERROR: + heap.free(h, rdr->seq); + heap.free(h, rdr); + return nil; +} + +error +bio·closeseq(bio·SeqReader *rdr) +{ + mem·Allocator heap; + void *h; + + heap = rdr->seq->heap; + h = rdr->seq->h; + + heap.free(h, rdr->seq); + heap.free(h, rdr); + + return 0; +} + + +static +error +readfasta(bio·SeqReader *rdr, bio·Seq *seq, byte hdr, byte stop) +{ + error err; + byte *beg; + + if (rdr->eof && rdr->b == rdr->bend-1) + return EOF; + + reset(rdr->seq); + + // NOTE: Can this case happen? + assert(rdr->b != rdr->bend); + if(*rdr->b++ != hdr) { + errorf("fasta/q format: expected '%c', found '%c'", hdr, *rdr->b--); + return 1; + } + +NAME: + beg = rdr->b; + while(rdr->b != rdr->bend) { + if(*rdr->b++ == '\n') { + push(&rdr->seq, (rdr->b - 1) - beg, beg); + goto SEQ; + } + } + + push(&rdr->seq, rdr->b - beg, beg); + + if(err = fill(rdr), err) { + errorf("read: could not populate buffer"); + return 1; + } + goto NAME; + +SEQ: + put(&rdr->seq, '\0'); + rdr->seq->off = rdr->seq->it - rdr->seq->b; + +SEQL: + beg = rdr->b; + while(rdr->b != rdr->bend) { + if(*rdr->b == '\n') { + push(&rdr->seq, rdr->b - beg, beg); + beg = rdr->b + 1; + } + + if(*rdr->b == stop || *rdr->b == '\0') + goto SUCCESS; + + rdr->b++; + } + + push(&rdr->seq, rdr->b - beg, beg); + + if(err = fill(rdr), err) { + errorf("read: could not populate buffer"); + return 1; + } + goto SEQL; + +SUCCESS: + push(&rdr->seq, rdr->b - beg, beg); + put(&rdr->seq, '\0'); + + return 0; +} + +/* + * fasta files + */ + +error +bio·readfasta(bio·SeqReader *rdr, bio·Seq *seq) +{ + error err; + + err = readfasta(rdr, seq, '>', '>'); + if(err && err != EOF) { + errorf("parse fail: could not read sequence of record"); + return err; + } + + seq->name = rdr->seq->b; + seq->s = rdr->seq->b + rdr->seq->off; + seq->len = rdr->seq->it - seq->s; + seq->q = nil; + + return err; +} + +/* + * fastq files + */ + +error +bio·readfastq(bio·SeqReader *rdr, bio·Seq *seq) +{ + int n; + byte *beg; + error err; + + err = readfasta(rdr, seq, '@', '+'); + if(err) { + errorf("parse fail: could not read sequence of record"); + return err; + } + + seq->len = rdr->seq->it - (rdr->seq->b + rdr->seq->off); + + if(*rdr->b++ != '+') { + errorf("format error: no '+' character seperator found"); + return -1; + } + +EATLN: + while(rdr->b != rdr->bend) { + if (*rdr->b++ == '\n') { + n = 0; + goto QUAL; + } + } + + if(err = fill((bio·SeqReader*)rdr), err) { + errorf("read: could not populate buffer"); + return 1; + } + goto EATLN; + +QUAL: + beg = rdr->b; + while(rdr->b != rdr->bend) { + if(*rdr->b == '\n') { + push(&rdr->seq, rdr->b - beg, beg); + beg = rdr->b + 1; + } + + if(n++ == seq->len || *rdr->b == '\0') { + err = *rdr->b == '\0' ? EOF : 0; + goto SUCCESS; + } + + rdr->b++; + } + + push(&rdr->seq, rdr->b - beg, beg); + + if(err = fill((bio·SeqReader*)rdr), err) { + errorf("read: could not populate buffer"); + return 1; + } + goto QUAL; + + +SUCCESS: + push(&rdr->seq, rdr->b - beg, beg); + put(&rdr->seq, '\0'); + + seq->name = rdr->seq->b; + seq->s = rdr->seq->b + rdr->seq->off; + seq->q = seq->s + seq->len + 1; + + return err; +} -- cgit v1.2.1