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#include <u.h>
#include <libn.h>
#include <libbio.h>
#include <time.h>
#include "kseq.h"
static
int
my_read(Stream *s, void *buf, int n)
{
return io·read(s, 1, n, buf);
}
KSEQ_INIT(Stream*, my_read)
// -----------------------------------------------------------------------
// Point of entry for testing
error
test·newick()
{
error err;
bio·Tree t;
mem·Arena *mem;
Stream *fd[2];
io·Peeker rdr;
io·Putter wtr;
mem·Allocator al;
mem = mem·newarena(mem·sys, nil);
rdr = (io·Peeker){.get = &io·getbyte, .unget = &io·ungetbyte};
wtr = (io·Putter){.put = &io·putbyte, .putstr = &io·putstring};
al = (mem·Allocator) { .alloc = &mem·arenaalloc, .free = nil, };
fd[0] = io·open("/home/nolln/root/data/test/example.nwk", "r");
fd[1] = io·open("/home/nolln/root/data/test/example.proc.nwk", "w");
t = bio·readnewick(rdr, fd[0], al, mem);
err = bio·writenewick(t, wtr, fd[1]);
io·flush(fd[1]);
io·close(fd[0]);
io·close(fd[1]);
mem·freearena(mem);
return 0;
}
error
test·fasta()
{
error err;
Stream *fd;
bio·Seq seq;
bio·FastaReader *rdr;
clock_t t;
fd = io·open("/home/nolln/root/data/test/zika.fa", "r");
/* Benchmark against Heng */
#if 0
int n, slen;
kseq_t *kseq;
t = clock();
kseq = kseq_init(fd);
while (kseq_read(kseq) >= 0) {
++n, slen += kseq->seq.l;
}
t = clock() - t;
printf("heng's code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
kseq_destroy(kseq);
io·seek(fd, 0, seek·set);
#endif
rdr = bio·openfasta((io·Reader){.read = &io·read}, fd, mem·sys, nil);
t = clock();
err = 0;
while (!err) {
err = bio·readfasta(rdr, &seq);
}
t = clock() - t;
printf("nick's code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
bio·closefasta(rdr);
io·close(fd);
return err <= 0 ? 0 : 1;
}
error
test·fastq()
{
error err;
Stream *fd;
bio·Seq seq;
bio·FastqReader *rdr;
clock_t t;
int n, slen;
kseq_t *kseq;
fd = io·open("/home/nolln/root/data/test/eg.fq", "r");
t = clock();
kseq = kseq_init(fd);
while (kseq_read(kseq) >= 0) {
++n, slen += kseq->seq.l;
}
t = clock() - t;
printf("heng's fastq code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
kseq_destroy(kseq);
io·seek(fd, 0, seek·set);
rdr = bio·openfastq((io·Reader){.read = &io·read}, fd, mem·sys, nil);
t = clock();
err = 0;
while (!err) {
err = bio·readfastq(rdr, &seq);
}
t = clock() - t;
printf("nick's fastq code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
bio·closefastq(rdr);
io·close(fd);
return err <= 0 ? 0 : 1;
}
error
main()
{
error err;
if (err = test·newick(), err) {
errorf("test fail: newick");
}
if (err = test·fasta(), err) {
errorf("test fail: fasta");
}
if (err = test·fastq(), err) {
errorf("test fail: fastq");
}
}
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