genomeGraph

package
v1.0.1 Latest Latest
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 Go to latest Published: May 1, 2024 License: BSD-3-Clause Imports: 22 Imported by: 0

Documentation

Overview

Package genomeGraph has structs and tools for reading, writing, editing and aligning graph representations of genomes

Index

Constants

This section is empty.

Variables

View Source 
var HumanChimpTwoScoreMatrix = [][]int64{
	{90, -330, -236, -356, -208},
	{-330, 100, -318, -236, -196},
	{-236, -318, 100, -330, -196},
	{-356, -236, -330, 90, -208},
	{-208, -196, -196, -208, -202},
}
View Source 
var HumanChimpTwoScoreMatrixNoGap = [][]int64{
	{90, -330, -236, -356},
	{-330, 100, -318, -236},
	{-236, -318, 100, -330},
	{-356, -236, -330, 90},
}

Functions

func AddEdge 

func AddEdge(u, v *Node, p float32)

AddEdge will append two edges one forward and one backwards for any two given node. Provide a probability float32 to specify a weight for an edge to describe the more likely path through the graph.

func AddPath 

func AddPath(allPaths []uint32, newPath uint32) []uint32

func AddSClip 

func AddSClip(front int, lengthOfRead int, cig []cigar.Cigar) []cigar.Cigar

func AllAreEqual 

func AllAreEqual(alpha []*Node, beta []*Node) bool

func AllAreEqualIgnoreOrder 

func AllAreEqualIgnoreOrder(alpha []*Node, beta []*Node) bool

func BasesInGraph 

func BasesInGraph(g *GenomeGraph) int

BasesInGraph will calculate the number of bases contained in GenomeGraph using dnaTwoBit.

func BlastSeed 

func BlastSeed(seed *SeedDev, read fastq.Fastq, scoreMatrix [][]int64) int64

func BreakNonContiguousGraph 

func BreakNonContiguousGraph(g []Node) [][]*Node

TODO: possible to order nodes while breaking discontiguous graphs??? BreakNonContiguousGraph will return a slice of graphs ([]*Node) such that each graph in the slice is contiguous.

func CatPaths 

func CatPaths(currPaths []uint32, newPaths []uint32) []uint32

func ChromAndPosToNumber 

func ChromAndPosToNumber(chrom int, start int) uint64

func CompareBlastScore 

func CompareBlastScore(a *SeedDev, b *SeedDev, read fastq.Fastq, scoreMatrix [][]int64) int

func CompareLenSeedDev 

func CompareLenSeedDev(a *SeedDev, b *SeedDev) int

func CompareSeedDev 

func CompareSeedDev(a *SeedDev, b *SeedDev) int

func GetSortOrder 

func GetSortOrder(g *GenomeGraph) []uint32

GetSortOrder will perform a breadth first search (BFS) on a graph and return an output slice where output[sortedIdx] = originalIdx.

func GirafPairToSam 

func GirafPairToSam(ag giraf.GirafPair) sam.MatePair

func GirafToSam 

func GirafToSam(ag *giraf.Giraf) sam.Sam

func GraphSmithWatermanMemPool 

func GraphSmithWatermanMemPool(gg *GenomeGraph, read fastq.FastqBig, seedHash map[uint64][]uint64, seedLen int, stepSize int, scoreMatrix [][]int64, m [][]int64, trace [][]rune, memoryPool **SeedDev) sam.Sam

func GraphSmithWatermanToGiraf 

func GraphSmithWatermanToGiraf(gg *GenomeGraph, read fastq.FastqBig, seedHash map[uint64][]uint64, seedLen int, stepSize int, matrix *MatrixAln, scoreMatrix [][]int64, seedPool *sync.Pool, dnaPool *sync.Pool, sk scoreKeeper, dynamicScore dynamicScoreKeeper, seedBuildHelper *seedHelper) *giraf.Giraf

func IndexGenomeIntoMap 

func IndexGenomeIntoMap(genome []Node, seedLen int, seedStep int) map[uint64][]uint64

func LeftAlignTraversal 

func LeftAlignTraversal(n *Node, seq []dna.Base, refEnd int, currentPath []uint32, extension int, read []dna.Base, scores [][]int64, matrix *MatrixAln, sk scoreKeeper, dynamicScore dynamicScoreKeeper, pool *sync.Pool) ([]cigar.ByteCigar, int64, int, int, []uint32)

func LeftDynamicAln 

func LeftDynamicAln(alpha []dna.Base, beta []dna.Base, scores [][]int64, matrix *MatrixAln, gapPen int64, dynamicScore dynamicScoreKeeper) (int64, []cigar.ByteCigar, int, int)

func LeftLocal 

func LeftLocal(alpha []dna.Base, beta []dna.Base, scores [][]int64, gapPen int64, m [][]int64, trace [][]rune) (int64, []cigar.Cigar, int, int, int, int)

func LocalView 

func LocalView(samLine *sam.Sam, ref []*Node) string

func MatrixSetup 

func MatrixSetup(size int) ([][]int64, [][]byte)

func MismatchStats 

func MismatchStats(scoreMatrix [][]int64) (int64, int64, int64, int64)

func ModifySamToString 

func ModifySamToString(aln sam.Sam, samflag bool, rname bool, pos bool, mapq bool, cig bool, rnext bool, pnext bool, tlen bool, seq bool, qual bool, extra bool) string

func NeedlemanWunsch 

func NeedlemanWunsch(alpha []dna.Base, beta []dna.Base, scores [][]int64, gapPen int64, m [][]int64, trace [][]rune) (int64, []cigar.Cigar)

func NewDnaPool 

func NewDnaPool() sync.Pool

func NewMemSeedPool 

func NewMemSeedPool() sync.Pool

func NodePosToReadPos 

func NodePosToReadPos(graph *GenomeGraph, read *giraf.Giraf, node uint32, pos uint32) uint32

func PathToSeq 

func PathToSeq(p giraf.Path, genome *GenomeGraph) []dna.Base

func PathToString 

func PathToString(allPaths []uint32) string

func PrintGraph 

func PrintGraph(gg *GenomeGraph)

PrintGraph will quickly print simpleGraph to standard out.

func RandGiraf 

func RandGiraf(graph *GenomeGraph, numReads int, readLen int, randSeed int64) []*giraf.Giraf

func RandLocation 

func RandLocation(genome *GenomeGraph) (uint32, uint32)

func RandLocationFast 

func RandLocationFast(genome *GenomeGraph, totalBases int) (uint32, uint32)

func RandPathFwd 

func RandPathFwd(genome *GenomeGraph, nodeIdx uint32, pos uint32, length int) ([]uint32, uint32, []dna.Base)

func RandSomaticMutations 

func RandSomaticMutations(graph *GenomeGraph, reads []*giraf.Giraf, numSomaticSNV int, AlleleFrequency float64, randSeed int64) ([]uint32, []uint32)

TODO: simulate indels.

func RandomPairedReads 

func RandomPairedReads(genome *GenomeGraph, readLength int, numReads int, numChanges int) []fastq.PairedEnd

func RandomReads 

func RandomReads(genome *GenomeGraph, readLength int, numReads int, numChanges int) []fastq.Fastq

func ReversePath 

func ReversePath(alpha []uint32)

func RightAlignTraversal 

func RightAlignTraversal(n *Node, seq []dna.Base, start int, currentPath []uint32, extension int, read []dna.Base, scoreMatrix [][]int64, matrix *MatrixAln, sk scoreKeeper, dynamicScore dynamicScoreKeeper, pool *sync.Pool) ([]cigar.ByteCigar, int64, int, int, []uint32)

func RightDynamicAln 

func RightDynamicAln(alpha []dna.Base, beta []dna.Base, scores [][]int64, matrix *MatrixAln, gapPen int64, dynamicScore dynamicScoreKeeper) (int64, []cigar.ByteCigar, int, int)

func RightLocal 

func RightLocal(alpha []dna.Base, beta []dna.Base, scores [][]int64, gapPen int64, m [][]int64, trace [][]rune) (int64, []cigar.Cigar, int, int, int, int)

func RoutineFqPairToGiraf 

func RoutineFqPairToGiraf(gg *GenomeGraph, seedHash map[uint64][]uint64, seedLen int, stepSize int, scoreMatrix [][]int64, input <-chan fastq.PairedEndBig, output chan<- giraf.GirafPair, wg *sync.WaitGroup)

func RoutineFqToGiraf 

func RoutineFqToGiraf(gg *GenomeGraph, seedHash map[uint64][]uint64, seedLen int, stepSize int, scoreMatrix [][]int64, inputChan <-chan fastq.FastqBig, outputChan chan<- giraf.Giraf, wg *sync.WaitGroup)

Goroutine worker functions.

func RoutineGirafToSam 

func RoutineGirafToSam(gg *GenomeGraph, seedHash map[uint64][]uint64, seedLen int, stepSize int, scoreMatrix [][]int64, input <-chan fastq.PairedEndBig, output chan<- sam.Sam, wg *sync.WaitGroup)

func RoutineGirafToSamSingle 

func RoutineGirafToSamSingle(gg *GenomeGraph, seedHash map[uint64][]uint64, seedLen int, stepSize int, scoreMatrix [][]int64, inputChan <-chan fastq.FastqBig, outputChan chan<- sam.Sam, wg *sync.WaitGroup)

func SetEvenWeights 

func SetEvenWeights(u *Node)

SetEvenWeights will loop through a slice of edges and set the probability weight divided by the length of the slice.

func SimpleWriteGirafPair 

func SimpleWriteGirafPair(filename string, input <-chan giraf.GirafPair, wg *sync.WaitGroup)

func SmithWaterman 

func SmithWaterman(alpha []dna.Base, beta []dna.Base, scores [][]int64, gapPen int64, m [][]int64, trace [][]rune) (int64, []cigar.Cigar, int64, int64, int64, int64)

func SoftClipBases 

func SoftClipBases(front int, lengthOfRead int, cig []cigar.ByteCigar) []cigar.ByteCigar

func SortBlastz 

func SortBlastz(seeds []*SeedDev, read fastq.Fastq, scoreMatrix [][]int64)

func SortById 

func SortById(seqs []*Node)

func SortBySeq 

func SortBySeq(seqs []*Node)

func SortSeedDevByLen 

func SortSeedDevByLen(seeds []*SeedDev)

func SortSeedDevByTotalLen 

func SortSeedDevByTotalLen(seeds []*SeedDev)

func SortSeedLen 

func SortSeedLen(seeds []SeedDev)

func ViewGraphAlignment 

func ViewGraphAlignment(g *giraf.Giraf, genome *GenomeGraph) string

func ViewMatrix 

func ViewMatrix(m [][]int64) string

func WrapPairGiraf 

func WrapPairGiraf(gg *GenomeGraph, fq fastq.PairedEndBig, seedHash map[uint64][]uint64, seedLen int, stepSize int, matrix *MatrixAln, scoreMatrix [][]int64, seedPool *sync.Pool, dnaPool *sync.Pool, sk scoreKeeper, dynamicScore dynamicScoreKeeper, seedBuildHelper *seedHelper) giraf.GirafPair

func Write 

func Write(filename string, sg *GenomeGraph)

Write function will process GenomeGraph and write the data to a file.

func WriteToGraphHandle 

func WriteToGraphHandle(file io.Writer, gg *GenomeGraph, lineLength int)

WriteToGraphHandle will help with any error handling when writing GenomeGraph to file.

Types

type Edge 

type Edge struct {
	Dest *Node
	Prob float32
}

Edge describes the neighboring nodes and a weighted probability of the more likely path.

type GenomeGraph 

type GenomeGraph struct {
	Nodes []Node
}

GenomeGraph struct contains a slice of Nodes.

func EmptyGraph 

func EmptyGraph() *GenomeGraph

EmptyGraph will allocate a new zero pointer to a simple graph and will allocate memory for the Nodes of the graph.

func Read 

func Read(filename string) *GenomeGraph

Read will process a simple graph formated text file and parse the data into graph fields.

func SortGraph 

func SortGraph(g *GenomeGraph) *GenomeGraph

SortGraph will reorder nodes in a graph such that the order and Ids of the output graph are topologically sorted.

func VariantGraph 

func VariantGraph(ref <-chan fasta.Fasta, vcfMap map[string][]vcf.Vcf) *GenomeGraph

type MatrixAln 

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

func NewSwMatrix 

func NewSwMatrix(size int) MatrixAln

type Node 

type Node struct {
	Id        uint32
	ColumnId  uint32
	Seq       []dna.Base        // only this field or the SeqThreeBit will be kept
	SeqTwoBit *dnaTwoBit.TwoBit // this will change to a ThreeBit or be removed
	Prev      []Edge
	Next      []Edge

} // used to have Name (string) and Info (Annotation)

Node is uniquely definded by Id and is encoded with information describing sequence order and orientation and annotated variance.

func AddNode 

func AddNode(g *GenomeGraph, n *Node) *Node

AddNode will add the values in n to the graph at the index of n.Id A pointer to the new location of the node (inside the graph) is returned.

func FaSeqToNode 

func FaSeqToNode(target fasta.Fasta, query fasta.Fasta, tStart int, qStart int, cigar align.Cigar, index int) (*Node, int, int)

FaSeqToNode is a general function used create a new node based on a target fasta, query fasta and a cigar operation. In addition, given two indices, it will update start/end for the subset of bases used to create the new Node. TODO: Add logic for correct node name annotation convention.

type ScoreMatrixHelper 

type ScoreMatrixHelper struct {
	Matrix                         [][]int64
	MaxMatch                       int64
	MinMatch                       int64
	LeastSevereMismatch            int64
	LeastSevereMatchMismatchChange int64
}

type SeedDev 

type SeedDev struct {
	TargetId    uint32
	TargetStart uint32
	QueryStart  uint32
	Length      uint32
	PosStrand   bool
	TotalLength uint32
	NextPart    *SeedDev
}

Source Files

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