Replace characters in sequences of input alignment using a regex.
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.SeqBag
// or var al align.Alignment if aligned sequences
/* First Alignment*/
/* Get reader (plain text or gzip) */
if fi, r, err = utils.GetReader("align.fa"); err != nil {
panic(err)
}
defer fi.Close()
/* Parse Fasta */
if al, err = fasta.NewParser(r).ParseUnalign(); err != nil {
/* for aligned seqs: if al, err = fasta.NewParser(r).Parse(); err != nil {*/
panic(err)
}
if err = al.Replace("GA.", "---", true); err != nil {
panic(err)
}
fmt.Println(fasta.WriteAlignment(al))
}