kseq
Functionality: a generic stream buffer & FASTA/FASTQ file parser
This kseq is download from https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/blob/master/src/kseq.h.
gz mode usage
This content is from http://attractivechaos.github.io/klib/#Kseq%3A%20stream%20buffer%20and%20FASTA%2FQ%20parser.
Synopsis
- Functionality: generic stream buffer & FASTA/FASTQ file parser
- Library source code: kseq.h
- Dependencies: none; zlib recommended, but not required
- Related articles: A generic stream buffer, What does zlib-1.2.5 bring to us? and How To Efficiently Parse A Huge Fastq File?
Examples
Example 1: parse FASTA/Q file, optionally compressed with zlib
// to compile: gcc this_prog.c -lz
#include <zlib.h>
#include <stdio.h>
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
int main(int argc, char *argv[])
{
gzFile fp;
kseq_t *seq;
int l;
if (argc == 1) {
fprintf(stderr, "Usage: %s <in.fasta>\n", argv[0]);
return 1;
}
fp = gzopen(argv[1], "r");
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
printf("name: %s\n", seq->name.s);
if (seq->comment.l) printf("comment: %s\n", seq->comment.s);
printf("seq: %s\n", seq->seq.s);
if (seq->qual.l) printf("qual: %s\n", seq->qual.s);
}
printf("return value: %d\n", l);
kseq_destroy(seq);
gzclose(fp);
return 0;
}Example 2: read a text file line-by-line
#include <zlib.h>
#include <stdio.h>
#include <stdlib.h>
#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)
int main(int argc, char *argv[])
{
gzFile fp;
kstream_t *ks;
kstring_t str = {0,0,0};
if (argc == 1) {
fprintf(stderr, "Usage: %s <in.txt>\n", argv[0]);
return 1;
}
fp = gzopen(argv[1], "r");
ks = ks_init(fp);
while (ks_getuntil(ks, '\n', &str, 0) >= 0)
printf("%s\n", str.s);
ks_destroy(ks);
gzclose(fp);
free(str.s);
return 0;
}Common file usage
See fileread.c for using kseq.h.
I made a simple solution for fileread.c in Visual Studio 2022, called kseq.sln.