func main() {
fasta, err := seqio.NewFastaReader(seq.RNAredundant, "hairpin.fa")
//fasta, err := seqio.NewFastaReader(seq.Unlimit, "test.fa")
if err != nil {
fmt.Println(err)
return
}
var records []*seqio.FastaRecord
// You can use Iterator or HasNext() - NextSeq() pair.
// for record := range fasta.Iterator(10) {
// fmt.Printf(">%s\n%s", record.Id, record.FormatSeq(70))
// }
for fasta.HasNext() {
record, err := fasta.NextSeq()
if err != nil { // invalid sequence
fmt.Println(err)
continue
}
s := record.Seq
// fmt.Printf(">%s\n%s\n", record.Id, record.Seq.Seq)
// format output
fmt.Printf(">%s\n%s", record.ID, record.FormatSeq(70))
// reverse complement
fmt.Printf("\nrevcom\n%s", seq.FormatSeq(s.Revcom().Seq, 70))
// length
fmt.Printf("Seq length: %d\n", s.Length())
// base content
fmt.Printf("GC content: %.2f\n", s.BaseContent("gc"))
fmt.Println()
records = append(records, record)
}
// write to file
writer := seqio.NewFastaWriter("tmp.fasta", 70)
writer.Write(records)
}
// FormatSeq formats output
func (record *FastaRecord) FormatSeq(width int) []byte {
return seq.FormatSeq(record.Seq.Seq, width)
}
