blast

Documentation

Index

• Variables
• func ExtractBest(bs Blast, p float64, fKing, fNames string) (Blast, Duplicated, error)
• func OrderedBy(less ...lessFunc) *multiSorter
• type Blast
  • func LoadBlast(file string) (Blast, error)
  • func (bs Blast) ExtractGenomes() map[string]map[string]bool
  • func (b Blast) GetPangenome(t pangenome.Taxids, core, acc float64, k, s string) pangenome.Pangenome
  • func (b Blast) Pretty(nb int)
  • func (b Blast) Write(d, o string) error
• type Duplicated
  • func (d Duplicated) PrintDup()
  • func (d Duplicated) Write(dir, o string) error

Variables

var AZqseqid = func(c1, c2 *row) bool {
	return c1.Qseqid <= c2.Qseqid
}

Closures that order the Change structure.

var AZsseqid = func(c1, c2 *row) bool {
	return c1.Sseqid <= c2.Sseqid
}

var IncEvalue = func(c1, c2 *row) bool {
	return c1.Evalue < c2.Evalue
}

var IncSstart = func(c1, c2 *row) bool {
	return c1.Sstart < c2.Sstart
}

var Length = func(c1, c2 *row) bool {
	return c1.Length > c2.Length
}

var Pident = func(c1, c2 *row) bool {
	return c1.Pident > c2.Pident
}

var Qcovhsp = func(c1, c2 *row) bool {
	return c1.Qcovhsp > c2.Qcovhsp
}

Functions

func ExtractBest

func ExtractBest(bs Blast, p float64, fKing, fNames string) (Blast, Duplicated, error)

func OrderedBy

func OrderedBy(less ...lessFunc) *multiSorter

OrderedBy returns a Sorter that sorts using the less functions, in order. Call its Sort method to sort the data.

Types

type Blast

type Blast []row

func LoadBlast

func LoadBlast(file string) (Blast, error)

func (Blast) ExtractGenomes

func (bs Blast) ExtractGenomes() map[string]map[string]bool

func (Blast) GetPangenome

func (b Blast) GetPangenome(t pangenome.Taxids, core, acc float64, k, s string) pangenome.Pangenome

func (Blast) Pretty

func (b Blast) Pretty(nb int)

func (Blast) Write

func (b Blast) Write(d, o string) error

type Duplicated

type Duplicated [][]*row

func (Duplicated) PrintDup

func (d Duplicated) PrintDup()

func (Duplicated) Write

func (d Duplicated) Write(dir, o string) error