Test Sequence Generator

ident.go

package main

import (
	"bufio"
	"math/rand"
	"os"

	"github.com/biogo/biogo/alphabet"
	"github.com/biogo/biogo/io/seqio/fasta"
	"github.com/biogo/biogo/seq/linear"
)

const alpbh = "ACGT"

func RandStringBytes(n int) string {
	b := make([]byte, n)
	for i := range b {
		b[i] = alpbh[rand.Intn(len(alpbh))]
	}
	return string(b)
}

func main() {

	seq := RandStringBytes(200)

	c := linear.NewSeq(
		"foo;size=100",
		[]alphabet.Letter(seq),
		alphabet.DNA,
	)

	f, _ := os.Create("test-identical.fasta")

	b := bufio.NewWriter(f)

	w := fasta.NewWriter(b, 80)

	for i := 0; i < 2000000; i++ {
		w.Write(c)
	}
}

uniq.go

package main

import (
	"bufio"
	"os"

	"github.com/biogo/biogo/alphabet"
	"github.com/biogo/biogo/io/seqio/fasta"
	"github.com/biogo/biogo/seq/linear"
)

const alpbh = "ACGT"

func combrep(n int, lst string) []string {
	if n == 0 {
		return []string{""}
	}
	if len(lst) == 0 {
		return nil
	}
	r := combrep(n, lst[1:])
	for _, x := range combrep(n-1, lst) {
		r = append(r, x+string(lst[0]))
	}
	return r
}

func main() {
	f, _ := os.Create("test-unique.fasta")

	b := bufio.NewWriter(f)

	w := fasta.NewWriter(b, 80)

	for _, s := range combrep(200, alpbh) {
		c := linear.NewSeq(
			"foo;size=100",
			[]alphabet.Letter(s),
			alphabet.DNA,
		)
		w.Write(c)
	}
}