cmd

Documentation

Index

• Constants
• Variables
• func CopyString(s string) string
• func Execute()
• func MaxInts(a int, vals ...int) int
• type Config
• type ProfileNode
• type Target
  • func (t *Target) AddTaxonomy(taxdb *taxdump.Taxonomy, showRanksMap map[string]interface{}, taxid uint32) bool
• type Targets
  • func (t Targets) Len() int
  • func (t Targets) Less(i, j int) bool
  • func (t Targets) Swap(i, j int)
• type TaxidChange
  • func (c TaxidChange) String() string
• type TaxidChangeCode
  • func (c TaxidChangeCode) String() string
• type TaxidChanges
  • func (changes TaxidChanges) Len() int
  • func (changes TaxidChanges) Less(i, j int) bool
  • func (changes TaxidChanges) Swap(i, j int)

Constants

const VERSION = "0.16.0"

VERSION of taxonkit

Variables

var RootCmd = &cobra.Command{
	Use:   "taxonkit",
	Short: "NCBI Taxonomy Toolkit",
	Long:  "",
}

RootCmd represents the base command when called without any subcommands

Functions

func CopyString

func CopyString(s string) string

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 MaxInts

func MaxInts(a int, vals ...int) int

Types

type Config

type Config struct {
	Threads      int
	OutFile      string
	DataDir      string
	NodesFile    string
	NamesFile    string
	DelNodesFile string
	MergedFile   string
	Verbose      bool
	LineBuffered bool
}

Config is the struct containing all global flags

type ProfileNode

type ProfileNode struct {
	Taxid         uint32
	Rank          string
	TaxonName     string
	LineageNames  []string // complete lineage
	LineageTaxids []uint32
	Abundance     float64
}

type Target

type Target struct {
	Taxid     uint32
	Abundance float64

	Rank          string
	TaxonName     string
	LineageNames  []string
	LineageTaxids []string

	CompleteLineageNames  []string
	CompleteLineageTaxids []uint32
}

func (*Target) AddTaxonomy

func (t *Target) AddTaxonomy(taxdb *taxdump.Taxonomy, showRanksMap map[string]interface{}, taxid uint32) bool

type Targets

type Targets []*Target

func (Targets) Len

func (t Targets) Len() int

func (Targets) Less

func (t Targets) Less(i, j int) bool

func (Targets) Swap

func (t Targets) Swap(i, j int)

type TaxidChange

type TaxidChange struct {
	Version       int16
	TaxidVersion  int16
	Change        TaxidChangeCode
	LineageTaxids []uint32
	ChangeValue   []uint32
}

TaxidChange means a taxid change record

func (TaxidChange) String

func (c TaxidChange) String() string

type TaxidChangeCode

type TaxidChangeCode uint32

TaxidChangeCode represents code of taxid change type

const (
	// TaxidUnchanged means taxid not changed
	TaxidUnchanged TaxidChangeCode = iota
	// TaxidNew means a new taxid
	TaxidNew
	// TaxidReuseDeleted means deleted taxids are reused again
	TaxidReuseDeleted
	// TaxidReuseMerged means merged taxids are reused again
	TaxidReuseMerged
	// TaxidDelete means a taxid is deleted
	TaxidDelete
	// TaxidMerge means a taxid is merged into another taxid
	TaxidMerge
	// TaxidAbsorb means another taxid is merged into this one
	TaxidAbsorb
	// TaxidNameChanged means scientific name is changed
	TaxidNameChanged
	// TaxidRankChanged means the rank is changed
	TaxidRankChanged
	// TaxidLineageChangedLin means lineage taxids remain, but lineage changed
	TaxidLineageChangedLin
	// TaxidLineageChangedTax means lineage taxids changed
	TaxidLineageChangedTax
	// TaxidLineageChangedLen means number of lineage taxids changed
	TaxidLineageChangedLen // number of lineage taxids changed
)

func (TaxidChangeCode) String

func (c TaxidChangeCode) String() string

type TaxidChanges

type TaxidChanges []TaxidChange

TaxidChanges represents a list of TaxidChange

func (TaxidChanges) Len

func (changes TaxidChanges) Len() int

func (TaxidChanges) Less

func (changes TaxidChanges) Less(i, j int) bool

func (TaxidChanges) Swap

func (changes TaxidChanges) Swap(i, j int)