dna

package
v0.3.7 Latest Latest
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 Go to latest Published: Nov 6, 2023 License: GPL-2.0 Imports: 6 Imported by: 0

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Index

Constants

View Source 
const (
	GAP_COUNT_NONE     = 0
	GAP_COUNT_INTERNAL = 1
	GAP_COUNT_ALL      = 2
)
View Source 
const (
	NT_DIST_OVER = 100000
)

Variables

This section is empty.

Functions

func BuildWeightsDirichlet 

func BuildWeightsDirichlet(al align.Alignment) []float64

Returns a vector of weights following a Dirichlet distribution D(n ; 1,...,1) 

with n alignment length

func BuildWeightsGamma 

func BuildWeightsGamma(al align.Alignment) []float64

Return a normalized vector of weights following a Gamma distribution

func DistMatrix 

func DistMatrix(al align.Alignment, weights []float64, model DistModel, range1Min, range1Max, range2Min, range2Max int,
	gamma bool, alpha float64, cpus int) (outmatrix [][]float64, err error)

DistMatrix computes a matrix distance, with weights associated to each alignment positions If weights == nil, then all weights are considered 1 range1, range2: To restrict the computation to the distances between these ranges of sequence IDS, based [range1Min,range1Max] vs. [range2Min, range2Max] If range1Min, range1Max, range2Min or range2Max are -1, then computes the usual half matrix

Types

type DistModel 

type DistModel interface {
	InitModel(al align.Alignment, weights []float64, gamma bool, alpha float64) error
	Distance(seq1 []uint8, seq2 []uint8, weigths []float64) (float64, error)
	Sequence(i int) ([]uint8, error)
}

func Model 

func Model(modelType string, removegaps bool) (model DistModel, err error)

Returns the right model depending on the args

type F81Model 

type F81Model struct {
	// contains filtered or unexported fields
}

func NewF81Model 

func NewF81Model(removegaps bool) *F81Model

func (*F81Model) Distance 

func (m *F81Model) Distance(seq1 []uint8, seq2 []uint8, weights []float64) (float64, error)

Distance computes F81 distance between 2 sequences

func (*F81Model) InitModel 

func (m *F81Model) InitModel(al align.Alignment, weights []float64, gamma bool, alpha float64) (err error)

func (*F81Model) Sequence added in v0.3.4 

func (m *F81Model) Sequence(i int) (seq []uint8, err error)

Sequence returns the ith sequence of the alignment encoded in int

type F84Model 

type F84Model struct {
	// contains filtered or unexported fields
}

func NewF84Model 

func NewF84Model(removegaps bool) *F84Model

func (*F84Model) Distance 

func (m *F84Model) Distance(seq1 []uint8, seq2 []uint8, weights []float64) (float64, error)

computes F84 distance between 2 sequences

func (*F84Model) InitModel 

func (m *F84Model) InitModel(al align.Alignment, weights []float64, gamma bool, alpha float64) (err error)

func (*F84Model) Sequence added in v0.3.4 

func (m *F84Model) Sequence(i int) (seq []uint8, err error)

Sequence returns the ith sequence of the alignment encoded in int

type JCModel 

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

func NewJCModel 

func NewJCModel(removegaps bool) *JCModel

func (*JCModel) Distance 

func (m *JCModel) Distance(seq1 []uint8, seq2 []uint8, weights []float64) (float64, error)

Distance computes JC69 distance between 2 sequences

func (*JCModel) InitModel 

func (m *JCModel) InitModel(al align.Alignment, weights []float64, gamma bool, alpha float64) (err error)

func (*JCModel) Sequence added in v0.3.4 

func (m *JCModel) Sequence(i int) (seq []uint8, err error)

Sequence returns the ith sequence of the alignment encoded in int

type K2PModel 

type K2PModel struct {
	// contains filtered or unexported fields
}

func NewK2PModel 

func NewK2PModel(removegaps bool) *K2PModel

func (*K2PModel) Distance 

func (m *K2PModel) Distance(seq1 []uint8, seq2 []uint8, weights []float64) (float64, error)

computes K2P distance between 2 sequences

func (*K2PModel) InitModel 

func (m *K2PModel) InitModel(al align.Alignment, weights []float64, gamma bool, alpha float64) (err error)

func (*K2PModel) Sequence added in v0.3.4 

func (m *K2PModel) Sequence(i int) (seq []uint8, err error)

Sequence returns the ith sequence of the alignment encoded in int

type PDistModel 

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

func NewPDistModel 

func NewPDistModel(removegaps bool) *PDistModel

func (*PDistModel) Distance 

func (m *PDistModel) Distance(seq1 []uint8, seq2 []uint8, weights []float64) (diff float64, err error)

computes p-distance between 2 sequences

func (*PDistModel) InitModel 

func (m *PDistModel) InitModel(al align.Alignment, weights []float64, gamma bool, alpha float64) (err error)

func (*PDistModel) Sequence added in v0.3.4 

func (m *PDistModel) Sequence(i int) (seq []uint8, err error)

Sequence returns the ith sequence of the alignment encoded in int

func (*PDistModel) SetCountGapMutations 

func (m *PDistModel) SetCountGapMutations(countgapmut int) (err error)

func (*PDistModel) SetRemoveAmbiguous added in v0.3.4 

func (m *PDistModel) SetRemoveAmbiguous(removeAmbiguous bool)

SetRemoveAmbiguous sets removeAmbiguous model variable if true, ambiguous positions are removed for the normalisation by the length for example: N vs. A : position not taken into account in length (can not decide wether there is a difference) R vs. Y : position taken into account in length (we know there is a difference)

type RawDistModel 

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

Like pdist, but without Normalization by the number of sites

func NewRawDistModel 

func NewRawDistModel(removegaps bool) *RawDistModel

func (*RawDistModel) Distance 

func (m *RawDistModel) Distance(seq1 []uint8, seq2 []uint8, weights []float64) (diff float64, err error)

Distance computes the number of differences between 2 sequences These differences include gaps vs. nt

func (*RawDistModel) InitModel 

func (m *RawDistModel) InitModel(al align.Alignment, weights []float64, gamma bool, alpha float64) (err error)

func (*RawDistModel) Sequence added in v0.3.4 

func (m *RawDistModel) Sequence(i int) (seq []uint8, err error)

Sequence returns the ith sequence of the alignment encoded in int

func (*RawDistModel) SetCountGapMutations 

func (m *RawDistModel) SetCountGapMutations(countgapmut int) (err error)

type TN82Model 

type TN82Model struct {
	// contains filtered or unexported fields
}

func NewTN82Model 

func NewTN82Model(removegaps bool) *TN82Model

func (*TN82Model) Distance 

func (m *TN82Model) Distance(seq1 []uint8, seq2 []uint8, weights []float64) (float64, error)

Distance computes TN82 distance between 2 sequences

func (*TN82Model) InitModel 

func (m *TN82Model) InitModel(al align.Alignment, weights []float64, gamma bool, alpha float64) (err error)

func (*TN82Model) Sequence added in v0.3.4 

func (m *TN82Model) Sequence(i int) (seq []uint8, err error)

Sequence returns the ith sequence of the alignment encoded in int

type TN93Model 

type TN93Model struct {
	// contains filtered or unexported fields
}

func NewTN93Model 

func NewTN93Model(removegaps bool) *TN93Model

func (*TN93Model) Distance 

func (m *TN93Model) Distance(seq1 []uint8, seq2 []uint8, weights []float64) (float64, error)

computes TN93 distance between 2 sequences

func (*TN93Model) InitModel 

func (m *TN93Model) InitModel(al align.Alignment, weights []float64, gamma bool, alpha float64) (err error)

func (*TN93Model) Sequence added in v0.3.4 

func (m *TN93Model) Sequence(i int) (seq []uint8, err error)

Sequence returns the ith sequence of the alignment encoded in int

Source Files

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