/
GSM.go
102 lines (88 loc) · 2.24 KB
/
GSM.go
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package main
import (
"os"
"fmt"
"bufio"
"bytes"
"sync"
"runtime"
"sort"
"io/ioutil"
"github.com/vtphan/kmers"
)
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 readGenome(filename string) []byte{
f,err := os.Open(filename)
if err != nil {
fmt.Printf("%v\n", err)
os.Exit(1)
}
defer f.Close()
br := bufio.NewReader(f)
byte_buffer := bytes.Buffer{}
_, isPrefix, err := br.ReadLine()
if err != nil || isPrefix {
fmt.Printf("%v\n", nil)
os.Exit(1)
}
for {
line, isPrefix, err := br.ReadLine()
if err != nil || isPrefix {
break
} else {
if bytes.Contains(line, []byte(">")) {
byte_buffer.Write([]byte("NNNNNNNNNNNNNN"))
} else {
byte_buffer.Write(line)
}
}
}
return byte_buffer.Bytes()
}