mean_qual.go

package main

// Import the standard formatting library:
import "fmt"

// Import the os library - needed for opening files:
import "os"

// Import the io library - needed for checking for EOF:
import "io"

//Import the necessary biogo fastq input/output library:
import (
	"github.com/biogo/biogo/alphabet"
	"github.com/biogo/biogo/io/seqio/fastq"
	"github.com/biogo/biogo/seq/linear"
)

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)

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

		var qtmp float64
		// For positions across the sequence:
		for i := 0; i < seq.Len(); i++ {
			// Acummulate error probabilities:
			qtmp += seq.At(i).Q.ProbE()
		}
		// Calculate mean error probability:
		mean_prob := qtmp / float64(seq.Len())
		// Calculate mean Q-score:
		mean_qual := alphabet.Ephred(mean_prob)
		fmt.Println(seq.CloneAnnotation().ID, "\t", byte(mean_qual))

	}
}