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@DisposaBoy
Created Oct 13, 2012
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package main
import (
"bufio"
"bytes"
"flag"
"fmt"
"github.com/drio/drio.go/common/files"
"io"
"log"
"os"
"runtime/pprof"
)
type record struct {
name, seq, qual []byte
}
func iterLines(r *bufio.Reader) func() ([]byte, bool) {
return func() ([]byte, bool) {
// note: this line simply creates two vars and then throw them away
// line, err := "", errors.New("")
// as far as i can see, the slice being copied so we can possibly speed
// things up even more by reusing the underlying array with r.ReadSlice
// line, err := r.ReadSlice('\n')
line, err := r.ReadBytes('\n')
if err != nil {
if err == io.EOF {
return line, true
} else {
fmt.Println(err)
os.Exit(1)
}
}
return line, false
}
}
// Original code: https://github.com/lh3/readfq
func ReadFq(r *bufio.Reader) func() (record, bool) {
var seq record
iter := iterLines(r)
last, done, finished := []byte{}, true, false
return func() (record, bool) {
if finished {
return seq, done
}
// Read the seq id (fasta or fastq)
if len(last) == 0 {
for l, done := iter(); !done; l, done = iter() {
if c := l[0]; c == '>' || c == '@' {
last = l[0 : len(l)-1]
break
}
}
}
if len(last) == 0 {
finished = true
return seq, done
}
seqName := bytes.Split(last[1:], []byte(" "))[0]
seq, last = record{name: seqName}, []byte{}
// Now read the sequence
for l, done := iter(); !done; l, done = iter() {
if c := l[0]; c == '+' || c == '>' || c == '@' {
last = l[0 : len(l)-1]
break
}
seq.seq = append(seq.seq, l[0:len(l)-1]...)
}
// We have a fasta record
if len(last) == 0 || last[0] != '+' {
return seq, !done
if len(last) == 0 {
return seq, done
}
} else { // this is a fastq record
leng := 0
for l, done := iter(); !done; l, done = iter() {
seq.qual = append(seq.qual, l[0:len(l)-1]...)
leng += len(l)
if leng >= len(seq.seq) { // we have read enough quality
last = []byte{}
return seq, done
}
}
}
finished = true
return seq, !done
}
}
var cpuprofile = flag.String("cpuprofile", "", "write cpu profile to file")
func main() {
flag.Parse()
if *cpuprofile != "" {
f, err := os.Create(*cpuprofile)
if err != nil {
log.Fatal(err)
}
pprof.StartCPUProfile(f)
defer pprof.StopCPUProfile()
}
// sample file found at https://wiki.cgb.indiana.edu/display/isga/Sample+FastQ+Files
fp, r := files.Xopen("sample_1.fq")
defer fp.Close()
n, sLen, qLen := 0, int64(0), int64(0)
iter := ReadFq(r)
for r, done := iter(); !done; r, done = iter() {
n += 1
sLen += int64(len(r.seq))
qLen += int64(len(r.qual))
}
fmt.Println(n, "\t", sLen, "\t", qLen)
}
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