Ejemplo n.º 1
0
func main() {
	runtime.GOMAXPROCS(runtime.NumCPU())
	switch kingpin.MustParse(app.Parse(os.Args[1:])) {
	case "host":
		StartHost()
	case "recv":
		StartRecv()
	default:
		kingpin.Usage()
	}

}
Ejemplo n.º 2
0
func main() {
	// Define the command-line structure using Kingpin
	var versionString = fmt.Sprintf("ceftools v%v.%v (C) 2015 Sten Linnarsson <http://linnarssonlab.org/>", ceftools.MajorVersion, ceftools.MinorVersion)

	var app = kingpin.New("cef", versionString)
	var app_bycol = app.Flag("bycol", "Apply command by columns instead of by rows").Short('c').Bool()
	var app_profile = app.Flag("profile", "Run with CPU profiling, output to the given file").String()

	var info = app.Command("info", "Show a summary of the file contents")
	var test = app.Command("test", "Perform an internal test")
	var transpose = app.Command("transpose", "Transpose rows and columns")
	var cmdimport = app.Command("import", "Import from a legacy format")
	var import_format = cmdimport.Flag("format", "The file format to expect ('strt')").Required().Short('f').String()

	var rename = app.Command("rename", "Rename attribute")
	var rename_attr = rename.Flag("attr", "The attribute to rename ('old=new')").Required().Short('c').String()

	var drop = app.Command("drop", "Remove attributes")
	var drop_attrs = drop.Flag("attrs", "Row attribute(s) to remove (case-sensitive, comma-separated)").Short('a').String()
	var drop_headers = drop.Flag("headers", "Headers to remove (case-sensitive, comma-separated)").Short('h').String()
	var drop_except = drop.Flag("except", "Keep the given attributes instead of dropping them ").Bool()

	var add = app.Command("add", "Add header or row attribute")
	var add_header = add.Flag("header", "Header to add, in the form 'name=value'").Short('h').String()
	var add_attr = add.Flag("attr", "Attribute to add, in the form 'name=value' (value can be '(row)')").Short('a').String()

	var cmdselect = app.Command("select", "Select rows that match criteria (and drop the rest)")
	var select_range = cmdselect.Flag("range", "Select a range of rows (like '10:90')").String()
	var select_where = cmdselect.Flag("where", "Select rows with specific value for attribute ('attr=value')").String()
	var select_except = cmdselect.Flag("except", "Invert selection").Bool()

	var rescale = app.Command("rescale", "Rescale values by rows")
	var rescale_method = rescale.Flag("method", "Method to use (log, tpm or rpkm)").Short('m').Required().Enum("log", "tpm", "rpkm")
	var rescale_length = rescale.Flag("length", "Indicate the name of the attribute that gives gene length (for RPKM)").String()

	var join = app.Command("join", "Join two files based on given attributes")
	var join_other = join.Flag("with", "The file to which the input should be joined").Required().String()
	var join_on = join.Flag("on", "The attributes on which to join, of form 'attr1=attr2'").Required().String()

	var sort = app.Command("sort", "Sort by row attribute or by specific column")
	var sort_by = sort.Flag("by", "The attribute or column ('column=value') to sort by").String()
	var sort_reverse = sort.Flag("reverse", "Sort in reverse order").Short('r').Bool()
	var sort_numerical = sort.Flag("numerical", "Numerical sort (default: alphabetical)").Short('n').Bool()
	var sort_spin = sort.Flag("spin", "Sort by SPIN").Bool()
	var sort_corrfile = sort.Flag("corrfile", "Optional filename where to write the sorted correlation matrix").String()

	var aggregate = app.Command("aggregate", "Calculate aggregate statistics per row")
	var aggregate_cv = aggregate.Flag("cv", "Calculate coefficient of variation (CV)").Bool()
	var aggregate_mean = aggregate.Flag("mean", "Calculate mean").Bool()
	var aggregate_stdev = aggregate.Flag("stdev", "Calculate standard deviation").Bool()
	var aggregate_max = aggregate.Flag("max", "Calculate max value").Bool()
	var aggregate_min = aggregate.Flag("min", "Calculate min value").Bool()
	var aggregate_noise = aggregate.Flag("noise", "Calculate noise (CV-vs-mean offset)").Required().Enum("std", "bands")

	var view = app.Command("view", "View the file content interactively")

	// Parse the command line
	var parsed, err = app.Parse(os.Args[1:])
	if err != nil {
		app.Usage(os.Stderr)
		return
	}

	if *app_profile != "" {
		f, err := os.Create(*app_profile)
		if err != nil {
			fmt.Fprintln(os.Stderr, err)
		}
		pprof.StartCPUProfile(f)
		defer pprof.StopCPUProfile()

	}

	// Handle the sub-commands
	switch kingpin.MustParse(parsed, nil) {
	case view.FullCommand():
		if err = ceftools.Viewer(*app_bycol); err != nil {
			fmt.Fprintln(os.Stderr, err)
		}
		return
	case aggregate.FullCommand():
		if err = ceftools.CmdAggregate(*aggregate_mean, *aggregate_cv, *aggregate_stdev, *aggregate_max, *aggregate_min, *aggregate_noise, *app_bycol); err != nil {
			fmt.Fprintln(os.Stderr, err)
		}
		return
	case rename.FullCommand():
		if err = ceftools.CmdRename(*rename_attr, *app_bycol); err != nil {
			fmt.Fprintln(os.Stderr, err)
		}
		return
	case add.FullCommand():
		if err = ceftools.CmdAdd(*add_attr, *add_header, *app_bycol); err != nil {
			fmt.Fprintln(os.Stderr, err)
		}
		return
	case sort.FullCommand():
		if *sort_spin {
			if err = ceftools.CmdSPIN(*sort_corrfile, *app_bycol); err != nil {
				fmt.Fprintln(os.Stderr, err)
			}
		} else {
			if err = ceftools.CmdSort(*sort_by, *sort_numerical, *sort_reverse, *app_bycol); err != nil {
				fmt.Fprintln(os.Stderr, err)
			}
		}
		return
	case join.FullCommand():
		if err = ceftools.CmdJoin(*join_other, *join_on, *app_bycol); err != nil {
			fmt.Fprintln(os.Stderr, err)
		}
		return
	case cmdimport.FullCommand():
		if *import_format == "strt" {
			if err = ceftools.CmdImportStrt(); err != nil {
				fmt.Fprintln(os.Stderr, err)
			}
		} else {
			fmt.Fprintln(os.Stderr, "Unknown format (only valid format is 'strt')")
		}
		return
	case cmdselect.FullCommand():
		if *select_range != "" {
			if *select_where != "" {
				fmt.Fprintln(os.Stderr, "Cannot select using --range and --where simultaneously (use a pipe)")
				return
			}
			temp := strings.Split(*select_range, ":")
			if len(temp) != 2 {
				fmt.Fprintln(os.Stderr, "Invalid range specification (should be like '1:10', ':20', or '100:')")
				return
			}
			from := 1
			if temp[0] != "" {
				from, err = strconv.Atoi(temp[0])
				if err != nil {
					fmt.Fprintln(os.Stderr, "Invalid range specification (should be like '1:10', ':20', or '100:')")
					return
				}
			}
			to := -1
			if temp[1] != "" {
				to, err = strconv.Atoi(temp[1])
				if err != nil {
					fmt.Fprintln(os.Stderr, "Invalid range specification (should be like '1:10', ':20', or '100:')")
					return
				}
			}
			if err := ceftools.CmdSelectRange(from, to, *app_bycol, *select_except); err != nil {
				fmt.Fprintln(os.Stderr, err.Error())
			}
			return
		}
		if *select_where != "" {
			if err := ceftools.CmdSelect(*select_where, *app_bycol, *select_except); err != nil {
				fmt.Fprintln(os.Stderr, err.Error())
			}
			return
		}
	case transpose.FullCommand():
		// Read the input
		var cef, err = ceftools.Read(os.Stdin, true)
		if err != nil {
			fmt.Fprintln(os.Stderr, err.Error())
			return
		}
		// Write the CEF file
		if err := ceftools.Write(cef, os.Stdout, false); err != nil {
			fmt.Fprintln(os.Stderr, err)
		}
		return
	case drop.FullCommand():
		if err = ceftools.CmdDrop(*drop_attrs, *drop_headers, *drop_except, *app_bycol); err != nil {
			fmt.Fprintln(os.Stderr, err)
		}
		return
	case rescale.FullCommand():
		if err = ceftools.CmdRescale(*rescale_method, *rescale_length, *app_bycol); err != nil {
			fmt.Fprintln(os.Stderr, err)
		}
		return

	// Perform test
	case test.FullCommand():
		var cef = new(ceftools.Cef)
		cef.Columns = 5
		cef.Rows = 10
		cef.Headers = make([]ceftools.Header, 2)
		cef.Headers[0].Name = "Tissue"
		cef.Headers[0].Value = "Amygdala"
		cef.Headers[1].Name = "Species"
		cef.Headers[1].Value = "Mouse"
		cef.ColumnAttributes = make([]ceftools.Attribute, 2)
		cef.ColumnAttributes[0].Name = "CellID"
		cef.ColumnAttributes[0].Values = []string{"A", "B", "C", "D", "E"}
		cef.ColumnAttributes[1].Name = "Well"
		cef.ColumnAttributes[1].Values = []string{"A01", "B03", "C09", "D12", "E21"}
		cef.RowAttributes = make([]ceftools.Attribute, 3)
		cef.RowAttributes[0].Name = "Gene"
		cef.RowAttributes[0].Values = []string{"Actb", "Gapdh", "Synpr", "Pou3f2", "Bdnf", "Ngf", "Sox11", "Olig1", "Olig2", "Foxj1"}
		cef.RowAttributes[1].Name = "Chromosome"
		cef.RowAttributes[1].Values = []string{"Chr0", "Chr1", "Chr2", "Chr3", "Chr4", "Chr5", "Chr6", "Chr7", "Chr8", "Chr9"}
		cef.RowAttributes[2].Name = "Length"
		cef.RowAttributes[2].Values = []string{"1200", "1300", "1400", "1700", "1920", "130", "800", "7800", "1100", "200"}
		cef.Matrix = make([]float32, 10*5)
		cef.Set(0, 0, 0)
		cef.Set(1, 0, 1)
		cef.Set(2, 0, 2)
		cef.Set(3, 0, 3)
		cef.Set(4, 0, 4)
		cef.Set(5, 0, 5)
		cef.Set(6, 0, 6)
		cef.Set(7, 0, 7)
		cef.Set(8, 0, 8)
		cef.Set(9, 0, 9)
		ceftools.Permute(cef, []int{0, 4, 2, 3, 1, 5, 6, 7, 8, 9}, []int{4, 3, 0, 1, 2})
		if err := ceftools.Write(cef, os.Stdout, false); err != nil {
			fmt.Fprintln(os.Stderr, err)
		}
		return

	// Show info
	case info.FullCommand():
		var cef, err = ceftools.Read(os.Stdin, *app_bycol)
		if err != nil {
			fmt.Fprintln(os.Stderr, err.Error())
			return
		}
		fmt.Fprintf(os.Stderr, "          Columns: %v\n", cef.Columns)
		fmt.Fprintf(os.Stderr, "             Rows: %v\n", cef.Rows)
		fmt.Fprintf(os.Stderr, "            Flags: %v\n", cef.Flags)
		fmt.Fprintln(os.Stderr, "          Headers:")
		for i := 0; i < len(cef.Headers); i++ {
			fmt.Fprint(os.Stderr, "                   ")
			fmt.Fprint(os.Stderr, cef.Headers[i].Name)
			fmt.Fprint(os.Stderr, " = ")
			fmt.Fprintf(os.Stderr, cef.Headers[i].Value)
			fmt.Fprint(os.Stderr, "\n")
		}
		fmt.Fprint(os.Stderr, "\n")
		fmt.Fprint(os.Stderr, "Column attributes: ")
		for i := 0; i < len(cef.ColumnAttributes); i++ {
			fmt.Fprint(os.Stderr, cef.ColumnAttributes[i].Name)
			if i != (len(cef.ColumnAttributes) - 1) {
				fmt.Fprint(os.Stderr, ", ")
			}
		}
		fmt.Fprint(os.Stderr, "\n")
		fmt.Fprint(os.Stderr, "   Row attributes: ")
		for i := 0; i < len(cef.RowAttributes); i++ {
			fmt.Fprint(os.Stderr, cef.RowAttributes[i].Name)
			if i != (len(cef.RowAttributes) - 1) {
				fmt.Fprint(os.Stderr, ", ")
			}
		}
		fmt.Fprintln(os.Stderr, "")
		return
	default:
		kingpin.Usage()
	}
}
Ejemplo n.º 3
0
func main() {
	cfg := new(initCfg)
	kingpin.Flag("n", "number of ipfs nodes to initialize").Short('n').IntVar(&cfg.Count)
	kingpin.Flag("port", "port to start allocations from").Default("4002").Short('p').IntVar(&cfg.PortStart)
	kingpin.Flag("force", "force initialization (overwrite existing configs)").Short('f').BoolVar(&cfg.Force)
	kingpin.Flag("mdns", "turn on mdns for nodes").BoolVar(&cfg.Mdns)
	kingpin.Flag("bootstrap", "select bootstrapping style for cluster").Default("star").StringVar(&cfg.Bootstrap)
	kingpin.Flag("utp", "use utp for addresses").BoolVar(&cfg.Utp)

	wait := kingpin.Flag("wait", "wait for nodes to come fully online before exiting").Bool()

	var args []string
	kingpin.Arg("args", "arguments").StringsVar(&args)
	kingpin.Parse()

	if len(args) == 0 {
		kingpin.Usage()
		return
	}

	switch args[0] {
	case "init":
		if cfg.Count == 0 {
			fmt.Printf("please specify number of nodes: '%s init -n 10'\n", os.Args[0])
			os.Exit(1)
		}
		err := IpfsInit(cfg)
		handleErr("ipfs init err: ", err)
	case "start":
		err := IpfsStart(*wait)
		handleErr("ipfs start err: ", err)
	case "stop", "kill":
		if len(args) > 1 {
			i, err := strconv.Atoi(args[1])
			if err != nil {
				fmt.Println("failed to parse node number: ", err)
				os.Exit(1)
			}
			err = KillNode(i)
			if err != nil {
				fmt.Println("failed to kill node: ", err)
			}
			return
		}
		err := IpfsKillAll()
		handleErr("ipfs kill err: ", err)
	case "restart":
		err := IpfsKillAll()
		handleErr("ipfs kill err: ", err)

		err = IpfsStart(*wait)
		handleErr("ipfs start err: ", err)
	case "shell":
		if len(args) < 2 {
			fmt.Println("please specify which node you want a shell for")
			os.Exit(1)
		}
		n, err := strconv.Atoi(args[1])
		handleErr("parse err: ", err)

		err = IpfsShell(n)
		handleErr("ipfs shell err: ", err)
	case "connect":
		if len(args) < 3 {
			fmt.Println("iptb connect [node] [node]")
			os.Exit(1)
		}

		from, err := parseRange(args[1])
		if err != nil {
			fmt.Printf("failed to parse: %s\n", err)
			return
		}

		to, err := parseRange(args[2])
		if err != nil {
			fmt.Printf("failed to parse: %s\n", err)
			return
		}

		for _, f := range from {
			for _, t := range to {
				err = ConnectNodes(f, t)
				if err != nil {
					fmt.Printf("failed to connect: %s\n", err)
					return
				}
			}
		}

	case "get":
		if len(args) < 3 {
			fmt.Println("iptb get [attr] [node]")
			os.Exit(1)
		}
		attr := args[1]
		num, err := strconv.Atoi(args[2])
		handleErr("error parsing node number: ", err)

		val, err := GetAttr(attr, num)
		handleErr("error getting attribute: ", err)
		fmt.Println(val)
	default:
		kingpin.Usage()
		fmt.Println(helptext)
		os.Exit(1)
	}
}