fastq_to_fasta.go

package main

// Import libraries:
import (
	"github.com/biogo/biogo/alphabet"
	"github.com/biogo/biogo/io/seqio/fasta"
	"github.com/biogo/biogo/io/seqio/fastq"
	"github.com/biogo/biogo/seq/linear"
	"io"
	"os"
)

func main() {
	// Open the fastq file specified on the command line
	// for reading:
	fh, err := os.Open(os.Args[1])
	// Check for open errors and abort:
	if err != nil {
		panic(err)
	}

	// Create a template seuence for the reader:
	template := linear.NewQSeq("", alphabet.QLetters{}, alphabet.DNA, alphabet.Sanger)
	// Create a fastq reader:
	reader := fastq.NewReader(fh, template)

	// Open the output file for writing:
	fho, err := os.Create(os.Args[2])
	// Close the file after we finished writing:
	defer fho.Close()
	if err != nil {
		panic(err)
	}
	// Create a fasta writer with width 80:
	writer := fasta.NewWriter(fho, 80)

	for {
		// Read the next fastq record:
		seq, err := reader.Read()
		// Break loop if we reached the end of the file:
		if err == io.EOF {
			break
		}
		// Write out the fasta record:
		writer.Write(seq)
	}
}