//Rosalind_0498 Rosalind_0442
//Rosalind_0498 Rosalind_2391
//Rosalind_2391 Rosalind_2323
func overlapGraph(filename string) (graph string) {
k := 3
reads := util.ReadFasta(filename)
prefixes := make(map[string][]string)
for id, seq := range reads {
prefix := seq[:k]
prefixes[prefix] = append(prefixes[prefix], id)
}
matches := make(map[string]struct{})
for id, seq := range reads {
suffix := seq[len(seq)-3:]
for _, match := range prefixes[suffix] {
if id != match {
//matches[id] = match
//matches += id + " " + match + "\n"
matches[id+" "+match] = struct{}{}
}
}
}
var keys []string
for k := range matches {
keys = append(keys, k)
}
sort.Strings(keys)
out := ""
for _, k := range keys {
out += k + "\n"
}
return out
}
//ATGCAACT
//A: 5 1 0 0 5 5 0 0
//C: 0 0 1 4 2 0 6 1
//G: 1 1 6 3 0 1 0 0
//T: 1 5 0 0 0 1 1 6
func consensusAndProfile(filename string) (result string) {
reads := util.ReadFasta(filename)
//fmt.Printf("reads: %v\n", reads)
letters := []rune{'A', 'C', 'G', 'T'}
var profile map[rune][]int
var rowlen int
for _, seq := range reads {
rowlen = len(seq)
if profile == nil {
profile = map[rune][]int{'A': make([]int, rowlen), 'T': make([]int, rowlen), 'G': make([]int, rowlen), 'C': make([]int, rowlen)}
}
for i, l := range seq {
profile[l][i]++
}
}
var consensus []rune
for i := range profile['A'] {
var winner rune
maxScore := 0
for _, k := range letters {
if profile[k][i] >= maxScore {
winner = k
maxScore = profile[k][i]
}
}
consensus = append(consensus, winner)
}
result = string(consensus) + "\n"
for _, l := range letters {
result += string(l) + ": " + strings.Trim(fmt.Sprintf("%v", profile[l]), "[]") + "\n"
}
//ioutil.WriteFile("test_data/consensusAndProfile.out", []byte(result), 0644)
return result
}