pangenome

Documentation

Index

• func LoadPangenome(f string) (Pangenome, Taxids, error)
• type Clusters
  • func (c Clusters) Write(o string) error
• type Converter
  • func ConversionTable(s [][]*node.Node) Converter
  • func (c Converter) GetClusters() Clusters
• type Counts
  • func (c Counts) Categorize(core, acc float64) string
  • func (c Counts) Csv() string
  • func (c Counts) Merge(m Counts) (Counts, error)
• type Gene
• type Pangenome
  • 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
  • func (s Summary) Print()
  • func (s Summary) Write(o string) error
• type Taxids

Functions

func LoadPangenome

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

Types

type Clusters

type Clusters map[string][]string

func (Clusters) Write

func (c Clusters) Write(o string) error

type Converter

type Converter map[string]string

func ConversionTable

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

func (Converter) GetClusters

func (c Converter) GetClusters() Clusters

type Counts

type Counts []int

func (Counts) Categorize

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

func (Counts) Csv

func (c Counts) Csv() string

func (Counts) Merge

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

type Gene

type Gene struct {
	Name     string
	Category string
	Counts   Counts
}

type Pangenome

type Pangenome map[string]*Gene

func (Pangenome) AccGenes

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

func (Pangenome) Cluster

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

func (Pangenome) CoreGenes

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

func (Pangenome) Pretty

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

func (Pangenome) SpecGenes

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

func (Pangenome) Summarize

func (p Pangenome) Summarize() Summary

func (Pangenome) Write

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

type Summary

type Summary struct {
	Core      int
	Accessory int
	Specific  int
}

func (Summary) Print

func (s Summary) Print()

func (Summary) Write

func (s Summary) Write(o string) error

type Taxids

type Taxids map[string]int