init

README.md

@@ -0,0 +1,26 @@
+# Batch Prokka Assemblies
+Batch Prokka can help you execute prokka batch assemblies.
+
+# Useage
+
+You only need to specify two parameters, dataPath and outPath.
+
+For example:
+
+```
+./batch-prokka-linux-amd64 -dataPath=/path/to/data -outPath=/path/to/out
+```
+
+The file name format example of the source file has been given in the [data directory](data).
+
+# Cross platform
+
+You can use this program directly on Linux, Windows and Mac, as long as your device has [Prokka](https://github.com/tseemann/prokka) installed.
+
+[window](batch-prokka-windows-amd64)
+
+[mac](batch-prokka-mac-amd64)
+
+[linux](batch-prokka-linux-amd64)
+
+

go.mod

@@ -0,0 +1,3 @@
+module gyy-prokka
+
+go 1.16

logfile.log

@@ -0,0 +1 @@
+2021/06/10 11:16:25 参数都要填噢!! 

main.go

@@ -0,0 +1,144 @@
+package main
+
+import (
+	"bufio"
+	"flag"
+	"fmt"
+	"io"
+	"io/ioutil"
+	"os"
+	"os/exec"
+	"sort"
+	"strings"
+	"time"
+)
+
+func main()  {
+	var outPath string
+	var dataPath string
+
+	flag.StringVar(&outPath, "outPath", "", "prokka output file path")
+	flag.StringVar(&dataPath, "dataPath", "", "prokka source file path")
+
+	flag.Parse()
+	if (len(outPath) == 0 || len(dataPath) == 0) {
+		logger("missing params !!")
+		return
+	}
+
+	var files []string
+	files, err := GetAllFile(dataPath, files)
+	if err != nil {
+		logger("read file error")
+		return
+	}
+
+	for _, file := range files {
+		length := strings.Index(file, ".")
+		outPutDirSeg := file[0:length]
+		desPath := outPath + "/" + outPutDirSeg + "_prokka"
+		_, err := os.Stat(desPath)
+
+		if os.IsNotExist(err) {
+			//ret := getGenArray(outPutDirSeg, files)
+			//file1 := ret[0]
+			//file2 := ret[1]
+
+			cmd := "prokka --compliant " + dataPath + "/" + file + " --outdir " + desPath
+
+			logger(cmd)
+			Command(cmd)
+		}
+
+	}
+
+
+
+}
+
+func Command(cmd string) error {
+	c := exec.Command("bash", "-c", cmd)
+	stdout, err := c.StdoutPipe()
+	if err != nil {
+		return err
+	}
+	go func() {
+		reader := bufio.NewReader(stdout)
+		for {
+			readString, err := reader.ReadString('\n')
+			if err != nil || err == io.EOF {
+				break
+			}
+			fmt.Print(readString)
+		}
+	}()
+	return c.Run()
+}
+
+func getGenArray(seg string, files []string) ([]string) {
+	var ret []string
+	for _, file := range files {
+		length := strings.Index(file, "_")
+		outPutDirSeg := file[0:length]
+		if seg == outPutDirSeg {
+			ret = append(ret, file)
+		}
+	}
+
+	sort.Sort(sort.StringSlice(ret))
+
+	return ret
+}
+
+func GetAllFile(pathname string, s []string) ([]string, error) {
+	rd, err := ioutil.ReadDir(pathname)
+	if err != nil {
+		fmt.Println("read dir fail:", err)
+		return s, err
+	}
+	for _, fi := range rd {
+		if fi.IsDir() {
+			fullDir := pathname + "/" + fi.Name()
+			s, err = GetAllFile(fullDir, s)
+			if err != nil {
+				fmt.Println("read dir fail:", err)
+				return s, err
+			}
+		} else {
+			//仅返回文件名
+			//fullName := pathname + "/" + fi.Name()
+			fullName := fi.Name()
+			s = append(s, fullName)
+		}
+	}
+	return s, nil
+}
+
+func logger(logthis string) {
+	filePath := "logfile.log"
+	fmt.Println(logthis)
+	_, err := os.Stat(filePath)
+	if os.IsNotExist(err) {
+		_, err := os.Create(filePath)
+		if err != nil {
+			fmt.Println(err)
+		}
+
+	}
+	file, err := os.OpenFile(filePath, os.O_WRONLY | os.O_TRUNC, 0666)
+	// file, err := os.OpenFile(filePath, os.O_WRONLY | os.O_APPEND, 0666)
+	if err != nil {
+		fmt.Printf("open file err=%v\n", err)
+		return
+	}
+
+	defer file.Close()
+
+	now := time.Now()
+	time := now.Format("2006/01/02 15:04:05")
+	str := fmt.Sprintf("%v %v ", time, logthis)
+	writer := bufio.NewWriter(file)
+	writer.WriteString(str)
+
+	writer.Flush()
+}