f2.go

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)
}