func main() {
br := bufio.NewReader(os.Stdin)
reads := []string{}
for {
line, err := br.ReadString('\n')
if err == io.EOF {
break
} else if err != nil {
log.Fatal(err)
}
reads = append(reads, strings.TrimSpace(line))
}
seen := map[string]int{}
for _, s := range reads {
seen[s] += 1
rc := gene.ReverseComplement(s)
if rc != s {
seen[rc] += 1
}
}
bases := ([]byte)("ACGT")
for _, s := range reads {
if seen[s] == 1 {
corrected := ""
for i := 0; i < len(s); i++ {
for _, b := range bases {
if s[i] != b {
t := s[:i] + string(b) + s[i+1:]
if seen[t] > 1 {
if corrected == "" {
corrected = t
} else {
log.Fatal("Found multiple corrections: " + s)
}
}
}
}
}
if corrected != "" {
fmt.Print(s, "->", corrected)
fmt.Println()
}
}
}
}
func main() {
k := flag.Int("k", 3, "Node substring length")
flag.Parse()
adj := map[string][]string{}
scanner := bufio.NewScanner(os.Stdin)
for scanner.Scan() {
read := scanner.Text()
if len(read) < *k+1 {
fmt.Fprintf(os.Stderr, "Error: Reads are too short for k.")
os.Exit(1)
}
for _, s := range []string{read, gene.ReverseComplement(read)} {
for i := 0; i < len(s)-*k; i++ {
u := s[i : i+*k]
v := s[i+1 : i+1+*k]
adj[u] = add(adj[u], v)
}
}
}
nonce := 1
fmt.Println("digraph debruijn {")
for u := range adj {
for _, v := range adj[u] {
if u == v {
fmt.Printf(" %s -> nonce%d;\n", u, nonce)
fmt.Printf(" nonce%d -> %s;\n", nonce, u)
nonce++
} else {
fmt.Printf(" %s -> %s;\n", u, v)
}
}
}
fmt.Println("}")
}
