pangenome

package module

v0.4.1-0...-92eedcb Latest Latest Go to latest Published: Feb 4, 2021 License: MIT Imports: 6 Imported by: 2

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func LoadPangenome(f string) (Pangenome, Taxids, error)

type Clusters map[string][]string

func (c Clusters) Write(o string) error

type Converter map[string]string

func ConversionTable(s [][]*node.Node) Converter

func (c Converter) GetClusters() Clusters

type Counts []int

func (c Counts) Categorize(core, acc float64) string

func (c Counts) Csv() string

func (c Counts) Merge(m Counts) (Counts, error)

type Gene struct {
	Name     string
	Category string
	Counts   Counts
}

type Pangenome map[string]*Gene

func (p Pangenome) AccGenes() map[string]bool

func (p Pangenome) Cluster(c Converter, core, acc float64) (Pangenome, error)

func (p Pangenome) CoreGenes() map[string]bool

func (p Pangenome) Pretty(nb int, t Taxids)

func (p Pangenome) SpecGenes() map[string]bool

func (p Pangenome) Summarize() Summary

func (p Pangenome) Write(o string, t Taxids) error

type Summary struct {
	Core      int
	Accessory int
	Specific  int
}

func (s Summary) Print()

func (s Summary) Write(o string) error

type Taxids map[string]int