gfa

a Go library for working with Graphical Fragment Assembly format

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Overview

This is a Go library for working with the Graphical Fragment Assembly (GFA) format.

The purpose of the GFA format is to capture sequence graphs as the product of an assembly, a representation of variation in genomes, splice graphs in genes, or even overlap between reads from long-read sequencing technology.

Read the GFA spec here.

Current limitations:

• restricted to GFA version 1
• does not handle the containment field
• validation is limited

Installation

go get github.com/will-rowe/gfa

Example usage

convert an MSA file to a GFA file

package main

import (
	"log"
	"os"

	"github.com/will-rowe/gfa"
)

var (
	inputFile = "./example.msa"
)

func main() {
	// open the MSA
	msa, _ := gfa.ReadMSA(inputFile)

	// convert the MSA to a GFA instance
	myGFA, err := gfa.MSA2GFA(msa)
	if err != nil {
		log.Fatal(err)
	}

	// create a gfaWriter
	outfile, err := os.Create("./example.gfa")
	defer outfile.Close()
	writer, err := gfa.NewWriter(outfile, myGFA)
	if err != nil {
		log.Fatal(err)
	}

	// write the GFA content
	if err := myGFA.WriteGFAContent(writer); err != nil {
		log.Fatal(err)
	}
}

process a GFA file line by line

package main

import (
	"flag"
	"io"
	"log"
	"os"

	"github.com/will-rowe/gfa"
)

var (
	inputFile = flag.String("inputFile", "", "input GFA file (empty for STDIN)")
)

func main() {
	flag.Parse()
	var r io.Reader

	// open file stream and close it when finished
	if *inputFile == "" {
		r = os.Stdin
	} else {
		fh, err := os.Open(*inputFile)
		if err != nil {
			log.Fatalf("could not open file %q:", err)
		}
		defer fh.Close()
		r = fh
	}

	// create a GFA reader
	reader, err := gfa.NewReader(r)
	if err != nil {
		log.Fatal("can't read gfa file: %v", err)
	}

	// collect the GFA instance
	myGFA := reader.CollectGFA()

	// check version and print the header / comment lines
	if myGFA.GetVersion() != 1 {
		log.Fatal("gfa file is not in version 1 format")
	}
	log.Println(myGFA.PrintHeader())
	if comments := myGFA.PrintComments(); comments != "" {
		log.Println(comments)
	}

	// read the GFA file
	for {
		line, err := reader.Read()
		if err == io.EOF {
			break
		}
		if err != nil {
			log.Fatal("error reading line in gfa file: %v", err)
		}

		// each line produced by Read() satisfies the gfaLine interface
		formattedLine := line.PrintGFAline()
		log.Printf("gfa line: %v", formattedLine)

		// you can also add the line to the GFA instance
		if err := line.Add(myGFA); err != nil {
			log.Fatal("error adding line to GFA instance: %v", err)
		}
	}
}