read_fastq_seq.go

package main

import (
	"fmt"
	"github.com/biogo/biogo/alphabet"
	"github.com/biogo/biogo/io/seqio/fastq"
	"github.com/biogo/biogo/seq/linear"
	"io"
	"os"
)

func main() {
	fh, err := os.Open(os.Args[1])
	if err != nil {
		panic(err)
	}

	template := linear.NewQSeq("", alphabet.QLetters{}, alphabet.DNA, alphabet.Sanger)
	reader := fastq.NewReader(fh, template)

	for {
		seq, err := reader.Read()
		if err == io.EOF {
			break
		}

		// Print the sequence ID and a tab:
		fmt.Print(seq.CloneAnnotation().ID, "\t")
		// For positions 0...9:
		for i := 0; i < 10; i++ {
			// Get the QLetter at position i:
			ql := seq.At(i)
			// Print the base at position i:
			fmt.Print(string(ql.L))
		}
		fmt.Println()
	}
}