cmd

Documentation

Index

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

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

`,
	PersistentPreRun: func(cmd *cobra.Command, args []string) {
		runtime.GOMAXPROCS(rootcpus)
		rootaligns = make(chan align.Alignment, 15)
		var fi *os.File
		var r *bufio.Reader
		var err error
		if infile == "stdin" || infile == "-" {
			fi = os.Stdin
		} else {
			fi, err = os.Open(infile)
			if err != nil {
				io.ExitWithMessage(err)
			}
		}
		if strings.HasSuffix(infile, ".gz") {
			if gr, err := gzip.NewReader(fi); err != nil {
				io.ExitWithMessage(err)
			} else {
				r = bufio.NewReader(gr)
			}
		} else {
			r = bufio.NewReader(fi)
		}
		var al align.Alignment
		var err2 error
		if rootphylip {
			go func() {
				err2 = phylip.NewParser(r).ParseMultiple(rootaligns)
				if err2 != nil {
					io.ExitWithMessage(err2)
				}
			}()
		} else {
			al, err2 = fasta.NewParser(r).Parse()
			if err2 != nil {
				io.ExitWithMessage(err2)
			}
			rootaligns <- al
			close(rootaligns)
		}
	},
}

RootCmd represents the base command when called without any subcommands

var Version string = "Unset"

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.