fastx

Overview ¶

Package fastx seamlessly parses FASTA and FASTQ format file This package seamlessly parses both FASTA and FASTQ formats.

## Examples

### Common operation

package main

import (
	"fmt"
	"io"
	"os"

	// "github.com/shenwei356/bio/seq"
	"github.com/shenwei356/bio/seqio/fastx"
	"github.com/shenwei356/xopen"
)

func main() {
	// use buffered out stream for output
	outfh, err := xopen.Wopen("-") // "-" for STDOUT
	checkError(err)
	defer outfh.Close()

	// disable sequence validation could reduce time when reading large sequences
	// seq.ValidateSeq = false

	reader, err := fastx.NewDefaultReader("-")
	checkError(err)
	for {
		record, err := reader.Read()
		if err != nil {
			if err == io.EOF {
				break
			}
			checkError(err)
			break
		}

		// fmt is slow for output, because it's not buffered
		// fmt.Printf("%s", record.Format(0))

		record.FormatToWriter(outfh, 0)
	}
}

func checkError(err error) {
	if err != nil {
		fmt.Fprintln(os.Stderr, err)
		os.Exit(1)
	}
}

***Note that***, similar with `bytes.Buffer.Bytes()` method, the current record will change after your another call of this method. You may use `record.Clone()` to make a copy.

### Asynchronously parsing

`ChunkChan` asynchronously reads FASTA/Q records, and returns a channel of Record Chunk, from which you can easily access the records. `bufferSize` is the number of buffered chunks, and `chunkSize` is the size of records in a chunk.

reader, err := fastx.NewDefaultReader(file)
checkError(err)

for chunk := range reader.ChunkChan(bufferSize, chunkSize) {
    checkError(chunk.Err)

    for _, record := range chunk.Data {
        fmt.Print(record)
    }
}

***Note that***, these's no need to clone the record by `record.Clone()` here.

### Custom alphabet and identifier regular expression

import (
    "github.com/shenwei356/bio/seq"
    "github.com/shenwei356/bio/seqio/fastx"
)

reader, err := fastx.NewReader(seq.DNA, file, "^([^\s]+)\s?")