/
nmw_stdin.go
153 lines (130 loc) · 3.1 KB
/
nmw_stdin.go
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package main
import (
"fmt"
//"strconv"
"strings"
"os"
"io/ioutil"
"runtime"
"sync"
nm "github.com/gglyptodon/needlemango"
)
func repeat() string {
bytes, err := ioutil.ReadAll(os.Stdin)
check(err)
return(string(bytes))
}
func readFromStdin() []byte{
bytes, err := ioutil.ReadAll(os.Stdin)
check(err)
return(bytes)
}
/*
MAIN
*/
func main(){
var stdinContent string
stdinContent = repeat()
var allA, allB []nm.Sequence
allA, allB = splitOnMarker(stdinContent,"")
//fmt.Println(stdinContent)
//allA = FastaReader{file:fastaFileA}.getSequences()
//allB = FastaReader{file:fastaFileB}.getSequences()
//allA = FastaReaderStd{inputString: stdinContent}.getSequences()
//allB = FastaReaderStd{inputString: stdinContent}.getSequences()
eblosum62 := nm.MakeSubstitutionMatrix("EBLOSUM62" )
eblosum62.SetMap("EBLOSUM62")
var maxCPU int = runtime.NumCPU()
var wg sync.WaitGroup
tasks :=make(chan Task,10000)
var resultStr []string
if (len(allA)*len(allB) < maxCPU){
maxCPU = len(allA)*len(allB)
}
for i := 0; i < maxCPU; i++ {
wg.Add(1)
go func() {
for t := range tasks {
resultStr = append(resultStr,nm.PrettyPrint(nm.Nmw(t.a,t.b,t.sm)))
}
wg.Done()
}()
}
var seen map[string]bool
seen = make(map[string]bool)
var ok bool
var tmpkey string
for _,a := range allA{
if a.GetSequence() ==""{continue}
for _,b:=range allB{
if b.GetSequence() ==""{continue}
tmpkey = b.GetHeader()+a.GetHeader()
ok = seen[tmpkey]
if ok{continue}
tmpkey = a.GetHeader()+b.GetHeader()
ok = seen[tmpkey]
if ok{continue}
seen[a.GetHeader()+b.GetHeader()]=true
seen[b.GetHeader()+a.GetHeader()]=true
tasks <- Task{a:a,b:b,sm:eblosum62}
}
}
close(tasks)
wg.Wait()
for _,v := range resultStr{
fmt.Print(v)
}
}
func Consumer(limit int, inChan <-chan Task){
for i := 0; i< limit;i++{
for s := range inChan {
fmt.Println(nm.PrettyPrint(nm.Nmw(s.a, s.b, s.sm)))
}
}
}
func Producer(allA []nm.Sequence, allB []nm.Sequence, sm nm.SubstitutionMatrix) <-chan Task {
ch := make(chan Task)
go func() {
for _,a :=range allA{
for _,b:= range allB{
ch <- Task{a,b,sm}
}
}
close(ch)
}()
return ch
}
func check(e error) {
if e != nil {
panic(e)
}
}
func splitOnMarker(text string, marker string)([]nm.Sequence, []nm.Sequence){
var resA []nm.Sequence
var resB []nm.Sequence
var pieces []string
if marker == "" {
marker = "終"
}
pieces = strings.Split(text, marker) //split in two pieces
tmpseq := strings.Split(pieces[0], ">")
for _,w := range(tmpseq){
var tmp []string
tmp = strings.Split(w,"\n")
shortHeader := strings.Split(tmp[0], " ")[0]
resA = append(resA, nm.MakeSequence(shortHeader, strings.Join(tmp[1:], "")))
}
tmpseq = strings.Split(pieces[1], ">")
for _,w := range(tmpseq){
var tmp []string
tmp = strings.Split(w,"\n")
shortHeader := strings.Split(tmp[0], " ")[0]
resB = append(resB, nm.MakeSequence(shortHeader, strings.Join(tmp[1:], "")))
}
return resA, resB
}
type Task struct{
a nm.Sequence
b nm.Sequence
sm nm.SubstitutionMatrix
}