prep

Documentation

Overview

Package used for preprocessing necessary data for the CAMUS algorithm

Index

• Variables
• func ConvertToNetwork(ntw *tree.Tree) (network *gr.Network, err error)
• func NetworkIsBinary(ntw *tree.Tree) bool
• func Preprocess(tre *tree.Tree, geneTrees []*tree.Tree, nprocs int, opts QuartetFilterOptions, ...) (*gr.TreeData, error)
• func TreeIsBinary(tre *tree.Tree) bool
• func WriteDPResultsToCSV(td *gr.TreeData, newicks []string, qsat []float64, w io.Writer) (err error)
• func WriteResultsLineplot(qstat []float64, prefix string) error
• func WriteRetScoresToCSV(scores []*map[string]float64, names []string) error
• type Format
  • func (f *Format) Set(s string) error
  • func (f Format) String() string
• type GeneTrees
  • func ReadInputFiles(treeFile, genetreesFile string, format Format) (*tree.Tree, *GeneTrees, error)
• type QMode
  • func (mode *QMode) Set(n int) error
  • func (mode QMode) String() string
• type QuartetFilterOptions
  • func SetQuartetFilterOptions(mode int, threshold float64) (QuartetFilterOptions, error)
  • func (opts QuartetFilterOptions) QuartetFilterOff() bool
• type Threshold
  • func (thresh Threshold) Keep(counts []uint32) bool
  • func (thresh *Threshold) Set(n float64) error
  • func (thresh Threshold) String() string

Variables

var (
	ErrInvalidFile     = errors.New("invalid file")
	ErrInvalidFormat   = errors.New("invalid format")
	ErrNoReticulations = errors.New("no reticulations")
	ErrWritingFile     = errors.New("error writing file")
)

var (
	ErrUnrooted     = errors.New("not rooted")
	ErrNonBinary    = errors.New("not binary")
	ErrMulTree      = errors.New("contains duplicate labels")
	ErrTypeOutRange = errors.New("out of type range")
)

var ParseFormat = map[string]Format{
	"newick": Newick,
	"nexus":  Nexus,
}

Functions

func ConvertToNetwork

func ConvertToNetwork(ntw *tree.Tree) (network *gr.Network, err error)

Read in extended newick file and make network

func NetworkIsBinary

func NetworkIsBinary(ntw *tree.Tree) bool

func Preprocess

func Preprocess(tre *tree.Tree, geneTrees []*tree.Tree, nprocs int, opts QuartetFilterOptions, minSupp float64) (*gr.TreeData, error)

Preprocess necessary data. Returns an error if the constraint tree is not valid (e.g., not rooted/binary) or if the gene trees are not valid (bad leaf labels).

func TreeIsBinary

func TreeIsBinary(tre *tree.Tree) bool

func WriteDPResultsToCSV

func WriteDPResultsToCSV(td *gr.TreeData, newicks []string, qsat []float64, w io.Writer) (err error)

Write DP results csv file to writer.

There are three columns: "Number of Branches", "Quartet Satisfied Percent", "Extended Newick"

func WriteResultsLineplot

func WriteResultsLineplot(qstat []float64, prefix string) error

func WriteRetScoresToCSV

func WriteRetScoresToCSV(scores []*map[string]float64, names []string) error

Write csv file containing reticulation branch scores to stdout

Types

type Format

type Format int

const (
	Newick Format = iota
	Nexus
)

func (*Format) Set

func (f *Format) Set(s string) error

func (Format) String

func (f Format) String() string

type GeneTrees

type GeneTrees struct {
	Trees []*tree.Tree // gene trees
	Names []string     // gene names
}

func ReadInputFiles

func ReadInputFiles(treeFile, genetreesFile string, format Format) (*tree.Tree, *GeneTrees, error)

Reads in and validates constraint tree and gene tree input files. Returns an error if the newick format is invalid, or the file is invalid for some other reason (e.g., more than one constraint tree)

type QMode

type QMode int

const (
	NonRestrictive QMode = iota + 1
	Restrictive
)

func (*QMode) Set

func (mode *QMode) Set(n int) error

func (QMode) String

func (mode QMode) String() string

type QuartetFilterOptions

type QuartetFilterOptions struct {
	// contains filtered or unexported fields
}

Options for quartet filter mode

func SetQuartetFilterOptions

func SetQuartetFilterOptions(mode int, threshold float64) (QuartetFilterOptions, error)

func (QuartetFilterOptions) QuartetFilterOff

func (opts QuartetFilterOptions) QuartetFilterOff() bool

type Threshold

type Threshold float64

func (Threshold) Keep

func (thresh Threshold) Keep(counts []uint32) bool

func (*Threshold) Set

func (thresh *Threshold) Set(n float64) error

func (Threshold) String

func (thresh Threshold) String() string