cmd

package
v0.1.2 Latest Latest
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Published: Oct 22, 2020 License: AFL-3.0, CC-BY-3.0 Imports: 30 Imported by: 0

Documentation

Index

Constants

This section is empty.

Variables

View Source
var ConvertCmd = &cobra.Command{
	Use:   "cvrt [xml1, xml2, ...]",
	Short: "Convert related functions.",
	Long:  `Convert related functions.`,
	Run: func(cmd *cobra.Command, args []string) {
		ConvertCmdRunOptions(cmd, args)
	},
}

ConvertCmd is the command line of bioctl Convert

View Source
var FmtClis = gfmt.ClisT{}

FmtClis is the parameters to run FmtCmd

View Source
var FmtCmd = &cobra.Command{
	Use:   "fmt [input1 input2]",
	Short: "A set of format (fmt) command.",
	Long:  `A set of format (fmt) command.`,
	Run: func(cmd *cobra.Command, args []string) {
		fmtCmdRunOptions(cmd, args)
	},
}

FmtCmd is the command line cobra object for basic re-format

View Source
var ParClis par.ClisT

ParClis is the parameters to run par.Tasks

View Source
var ParCmd = &cobra.Command{
	Use:   "par",
	Short: "Run parallel tasks.",
	Long:  `Run parallel tasks.`,
	Run: func(cmd *cobra.Command, args []string) {
		ParClis.Verbose = rootClis.Verbose
		ParClis.SaveLog = rootClis.SaveLog
		ParClis.TaskID = rootClis.TaskID
		ParClis.LogDir = rootClis.LogDir
		parCmdRunOptions(cmd, args)
	},
}

ParCmd is the command line of bioctl par

View Source
var PlotCmd = &cobra.Command{
	Use:   "plot",
	Short: "Plots related functions.",
	Long:  `Plots related functions.`,
	Run: func(cmd *cobra.Command, args []string) {
		plotCmdRunOptions(cmd, args)
	},
}

PlotCmd is the command line of bioctl plot

View Source
var RandCmd = &cobra.Command{
	Use:   "rand",
	Short: "Functions related to random events.",
	Long:  `Functions related to random events.`,
	Run: func(cmd *cobra.Command, args []string) {
		RandCmdRunOptions(cmd, args)
	},
}

RandCmd is the command line of bioctl Rand

View Source
var RangeCmd = &cobra.Command{
	Use:   "range [start end step]",
	Short: "Functions to manipulate intervals.",
	Long:  `Functions to manipulate intervals.`,
	Run: func(cmd *cobra.Command, args []string) {
		RangeCmdRunOptions(cmd, args)
	},
}

RangeCmd is the command line of bioctl Range

View Source
var StatCmd = &cobra.Command{
	Use:   "stat",
	Short: "Functions related to stat.",
	Long:  `Functions related to stat.`,
	Run: func(cmd *cobra.Command, args []string) {
		StatCmdRunOptions(cmd, args)
		if rootClis.HelpFlags {
			cmd.Help()
		}
	},
}

StatCmd is the command line of bioctl Stat

View Source
var StatDfCmd = &cobra.Command{
	Use:   "statdf",
	Short: "Functions related to stat data.frame.",
	Long:  `Functions related to stat data.frame.`,
	Run: func(cmd *cobra.Command, args []string) {
		StatDfCmdOptions(cmd, args)
		if rootClis.HelpFlags {
			cmd.Help()
		}
	},
}

StatDfCmd is the command line of bioctl statdf

View Source
var StatFnClis = StatFnClisT{}

StatFnClis is the parameters to run StatFnCmd

View Source
var StatFnCmd = &cobra.Command{
	Use:   "statfn",
	Short: "Functions related to stat file.",
	Long:  `Functions related to stat file.`,
	Run: func(cmd *cobra.Command, args []string) {
		StatFnCmdOptions(cmd, args)
		if rootClis.HelpFlags {
			cmd.Help()
		}
	},
}

StatFnCmd is the command line of bioctl statfn

Functions

func ConvertCmdRunOptions

func ConvertCmdRunOptions(cmd *cobra.Command, args []string)

func Execute

func Execute()

Execute main interface of bget

func RandCmdRunOptions

func RandCmdRunOptions(cmd *cobra.Command, args []string)

func RangeCmdRunOptions

func RangeCmdRunOptions(cmd *cobra.Command, args []string)

func StatCmdRunOptions

func StatCmdRunOptions(cmd *cobra.Command, args []string)

func StatDfCmdOptions

func StatDfCmdOptions(cmd *cobra.Command, args []string)

func StatFnCmdOptions

func StatFnCmdOptions(cmd *cobra.Command, args []string)

Types

type ConvertClisT

type ConvertClisT struct {
	NcbiXMLToJSON string
	NcbiXMLPaths  []string
	NcbiKeywords  string
}

ConvertClisT is the type to run bioctl Convert

var ConvertClis ConvertClisT

ConvertClis is the parameters to run par.Tasks

type PlotClisT

type PlotClisT struct {
	ThemeName      string
	ShowThemes     bool
	ShowThemesName bool
}

PlotClisT is the type to run bioctl plot

var PlotClis PlotClisT

PlotClis is the parameters to run par.Tasks

type RandClisT

type RandClisT struct {
	UUID   bool
	Date   bool
	String bool
	Int    bool
	Float  bool
	Length int
	Number int
}

RandClisT is the type to run bioctl Rand

var RandClis RandClisT

RandClis is the parameters to run par.Tasks

type RangeClisT

type RangeClisT struct {
	Start       float64
	StartChar   string
	EndChar     string
	End         float64
	Step        float64
	RefSequence string
	Sep         string
	Mode        string
}

RangeClisT is the type to run bioctl Range

var RangeClis RangeClisT

RangeClis is the parameters to run par.Tasks

type RootClisT

type RootClisT struct {
	// version of bioctl
	Version string
	Verbose int
	SaveLog bool
	TaskID  string
	LogDir  string
	Clean   bool
	Out     string
	Thread  int

	Uncompress string
	HelpFlags  bool
}

RootClisT is the bioctl global flags

type StatClisT

type StatClisT struct {
	Max           bool
	Min           bool
	Median        bool
	Mean          bool
	Mfreq         bool
	Variance      bool
	Sum           bool
	Pearson       bool
	Percentile    float64
	Freq          bool
	CuSum         bool
	GeometricMean bool
	HarmonicMean  bool
	Entropy       bool
	Covariance    bool
	SplitArgs     string
}

StatClisT is the type to run bioctl Stat

var StatClis StatClisT

StatClis is the parameters to run stat

type StatDfClisT

type StatDfClisT struct {
	Print      bool
	Header     string
	At         string
	SheetIndex int
}

StatDfClisT is the type to run bioctl statdf

var StatDfClis StatDfClisT

StatDfClis is the parameters to run statdf

type StatFnClisT

type StatFnClisT struct {
	// CountLines run the countLine()
	CountLines bool
	CountChars bool
	CountBytes bool
	CountWords bool
}

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