func main() {
if len(os.Args) != 2 {
panic("must provide sequence folder file.")
}
files, _ := ioutil.ReadDir(os.Args[1])
gsm := make(map[int]int)
numCores := runtime.NumCPU()
runtime.GOMAXPROCS(numCores)
kmer_len := 14
for index, file := range files {
genome := readGenome(os.Args[1] + "/" + file.Name())
var wg sync.WaitGroup
result := make(chan int, numCores)
for i := 0; i < numCores; i++ {
wg.Add(1)
go func(i int) {
defer wg.Done()
start := len(genome) * i / numCores
end := len(genome) * (i + 1) / numCores
if start != 0 {
start = start - kmer_len
}
fmt.Println(start, end)
kmers.Slide(genome, kmer_len, start, end, result)
}(i)
}
go func() {
wg.Wait()
close(result)
}()
for k := range result {
if gsm[k] == 0 {
gsm[k] = index + 1
} else if gsm[k] == index+1 {
} else {
gsm[k] = -1
}
}
}
var keys []int
for k := range gsm {
keys = append(keys, k)
}
sort.Ints(keys)
for _, k := range keys {
fmt.Println("Key:", kmers.NumToKmer(k, kmer_len), k, "Value:", gsm[k], "end")
}
}
func main() {
if len(os.Args) != 3 {
panic("Must provide sequence folder and result file name.")
}
kmer_len := 16
files, _ := ioutil.ReadDir(os.Args[1])
resultfile, err := os.Create(os.Args[2] + ".csv")
if err != nil {
fmt.Printf("%v\n", err)
os.Exit(1)
}
rw := csv.NewWriter(resultfile)
head := make([]string, len(files)+1)
head[0] = "kmer"
for index, fi := range files {
head[index+1] = fi.Name()
}
returnError := rw.Write(head)
if returnError != nil {
fmt.Println(returnError)
}
rw.Flush()
numCores := runtime.NumCPU()
runtime.GOMAXPROCS(numCores)
globalOccu := make(map[int]int16)
for _, file := range files {
localFreq := make(map[int]int32)
kmerFreq(file.Name(), localFreq, kmer_len)
for k := range localFreq {
globalOccu[k]++
}
}
topKnum := 100
var item *Item
kmernum := topKnum * len(files)
topK := make([]int, kmernum)
for i := range topK {
topK[i] = -1
}
m := 0
for _, file := range files {
fmt.Println(file.Name())
localFreq := make(map[int]int32)
kmerFreq(file.Name(), localFreq, kmer_len)
pq := make(PriorityQueue, topKnum)
k := 0
for j := range localFreq {
if !contains(topK, j) {
if k < topKnum {
pq[k] = &Item{
value: j,
priority: []int{int(globalOccu[j]), int(localFreq[j])},
index: k,
}
k++
if k == topKnum {
heap.Init(&pq)
}
} else {
item = &Item{
value: j,
priority: []int{int(globalOccu[j]), int(localFreq[j])},
}
if compare(item.priority, pq[0].priority) {
_ = heap.Pop(&pq).(*Item)
heap.Push(&pq, item)
}
}
}
}
for pq.Len() > 0 {
item := heap.Pop(&pq).(*Item)
fmt.Println(kmers.NumToKmer(item.value, kmer_len))
topK[m] = item.value
m++
}
}
matrix := make([][]int, kmernum)
for i := 0; i < kmernum; i++ {
matrix[i] = make([]int, len(files))
}
for index, file := range files {
localFreq := make(map[int]int32)
kmerFreq(file.Name(), localFreq, kmer_len)
for i := 0; i < kmernum; i++ {
matrix[i][index] = int(localFreq[topK[i]])
}
}
for i := 0; i < kmernum; i++ {
head[0] = strconv.Itoa(topK[i])
for j := 1; j < len(files)+1; j++ {
head[j] = strconv.Itoa(matrix[i][j-1])
}
returnError := rw.Write(head)
if returnError != nil {
fmt.Println(returnError)
}
rw.Flush()
}
resultfile.Close()
}