cmd

Documentation

Index

• Variables
• func Execute()
• func Readln(r *bufio.Reader) (string, error)

Variables

var RootCmd = &cobra.Command{
	Use:   "gotree",
	Short: "gotree: A set of tools to handle phylogenetic trees in go",
	Long: `gotree is a set of tools to handle phylogenetic trees in go.

Different usages are implemented: 
- Generating random trees
- Transforming trees (renaming tips, pruning/removing tips)
- Comparing trees (computing bootstrap supports, counting common edges)
`,
	PersistentPreRun: func(cmd *cobra.Command, args []string) {
		switch rootInputFormat {
		case "newick":
			treeformat = utils.FORMAT_NEWICK
		case "nexus":
			treeformat = utils.FORMAT_NEXUS
		case "phyloxml":
			treeformat = utils.FORMAT_PHYLOXML
		case "nextstrain":
			treeformat = utils.FORMAT_NEXTSTRAIN
		default:
			treeformat = utils.FORMAT_NEWICK
		}
		if seed == -1 {
			seed = time.Now().UTC().UnixNano()
		}
		rand.Seed(seed)
	},

	Run: func(cmd *cobra.Command, args []string) {
		s := cobrashell.New()

		s.Println(fmt.Sprintf("Welcome to Gotree Console %s", Version))
		s.Println("type \"help\" to get a list of available commands")
		cobrashell.AddCommands(s, cmd.Root(), nil, cmd.Root().Commands()...)

		s.Run()
	},

	PersistentPostRun: func(cmd *cobra.Command, args []string) {
	},
}

RootCmd represents the base command when called without any subcommands

var Version string

Version defines the version of gotree It is initialized during compilation with -ldflags "-X github.com/evolbioinfo/gotree/cmd.Version=Major.Minor..."

Functions

func Execute

func Execute()

Execute adds all child commands to the root command sets flags appropriately. This is called by main.main(). It only needs to happen once to the rootCmd.

func Readln

func Readln(r *bufio.Reader) (string, error)

Readln returns a single line (without the ending \n) from the input buffered reader. An error is returned iff there is an error with the buffered reader.