cmd

Documentation

Index

• Variables
• func Execute()

Variables

var RootCmd = &cobra.Command{
	Use:   "goalign",
	Short: "goalign: A set of tools to handle sequence alignments",
	Long: `goalign: A set of tools to handle sequence alignments.

It allows to :
1 - Convert formats
2 - Shuffle alignments
3 - Sample alignments
4 - Print informations about alignments
5 - Generate bootstrap alignments

Input alignment file formats:
1. Fasta (default)
2. Phylip (-p option)
3. Nexus (-x option)
4. Clustal (-u option)
4. Auto detect (--auto-detect option). In that case, it will test input formats in the following order:
    1. Fasta
    2. Nexus
    3. Phylip
    4. Clustal
    If none of these formats is recognized, then will exit with an error 

Please note that in --auto-detect mode, phylip format is considered as not strict!
`,
	PersistentPreRun: func(cmd *cobra.Command, args []string) {
		runtime.GOMAXPROCS(rootcpus)
		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 Goalign Console %s", version.Version))
		s.Println("type \"help\" to get a list of available commands")
		cobrashell.AddCommands(s, cmd.Root(), nil, cmd.Root().Commands()...)

		s.Run()
	},
}

RootCmd represents the base command when called without any subcommands

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.