Extracting sub-alignment (position 10 0-based inclusive, and with length 15) from an input alignment:
package main
import (
"bufio"
"fmt"
"io"
"github.com/evolbioinfo/goalign/align"
"github.com/evolbioinfo/goalign/io/fasta"
"github.com/evolbioinfo/goalign/io/utils"
)
func main() {
var fi io.Closer
var r *bufio.Reader
var err error
var al align.Alignment
var subalign align.Alignment = nil
/* Get reader (plain text or gzip) */
fi, r, err = utils.GetReader("align.fa")
if err != nil {
panic(err)
}
/* Parse Fasta */
al, err = fasta.NewParser(r).Parse()
if err != nil {
panic(err)
}
fi.Close()
/* Subalignment from position 10 (0-based inclusive),
and with length 15 */
subalign, err = al.SubAlign(10, 15)
if err != nil {
panic(err)
}
/* Printing alignment in Fasta */
fmt.Print(fasta.WriteAlignment(subalign))
}