gonetics

package module
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 Go to latest Published: Aug 14, 2020 License: GPL-3.0 Imports: 24 Imported by: 9

README

Gonetics

Gonetics is a bioinformatics library for the Go programming language (golang). It provides native data structures for handling genetic data and methods for handling common file formats such as BAM, GTF, BED, BigWig, and Wig. The documentation is available here.

Tools

Executables are available here.

Tool Description
bamCheckBin check bin records of a bam file
bamGenome print the genome (sequence table) of a bam file
bamToBigWig convert bam to bigWig (estimate fragment length if required)
bamView print contents of a bam file
bigWigEditChromNames edit chromosome names of a bigWig file (i.e. replace chr1 by just 1)
bigWigExtract extract regions from a bigWig file and save them as table or bigWig file
bigWigExtractChroms extract a subset of the chromosomes from a bigWig file
bigWigGenome print the genome (sequence table) of a bigWig file
bigWigHistogram compute a histogram of the values in a bigWig file
bigWigNil read bigWig and output it to a new file
bigWigMap apply a function to a set of bigWig files
bigWigPositive simple peak finding (i.e. every region with a value above a threshold)
bigWigQuantileNormalize quantile normalize a bigWig file to a reference
bigWigQuery retrieve data from a bigWig file
bigWigQuerySequence retrieve sequences from a bigWig file
bigWigStatistics compute summary statistics of a bigWig file
chromHmmTablesToBigWig convert chromHmm output (posteriors / binariezed bams) to bigWig
countKmers count kmers in a set of DNA sequences
drawGenomicRegions draw random genomic regions
fastaExtract extract regions from a fasta file
fastaUnresolvedRegions identify regions that are not resolved (i.e. stretches of 'NNNN...')
gtfToBed convert GTF files to Bed6 format
memeExtract extract PWM/PPM motifs from MEME/DREME xml files
observedOverExpectedCpG compute CpG scores as defined by Gardiner-Garden and Frommer (1987)
pwmScanSequences scan sequences for PWM hits
pwmScanRegions scan regions for multiple PWMs
segmentationDifferential extract differential regions from multiple chromatin segmentations

GRanges

Create a GRanges object with three ranges on the first chromosome:

  seqnames := []string{"chr1", "chr1", "chr1"}
  from     := []int{100000266, 100000271, 100000383}
  to       := []int{100000291, 100000296, 100000408}
  strand   := []byte{'+', '+', '-'}

  granges  := NewGRanges(seqnames, from, to, strand)
  fmt.Println(granges)

  seqnames                 ranges strand
1     chr1 [100000266, 100000291)      +
2     chr1 [100000271, 100000296)      +
3     chr1 [100000383, 100000408)      -

Add some meta data to the GRanges object:

  granges.AddMeta("data", []float64{1.0, 2.0, 3.0})

  seqnames                 ranges strand |          data
1     chr1 [100000266, 100000291)      + |      1.000000
2     chr1 [100000271, 100000296)      + |      2.000000
3     chr1 [100000383, 100000408)      - |      3.000000

Find overlaps of two GRanges objects:

  rSubjects := NewGRanges(
    []string{"chr4", "chr4", "chr4", "chr4"},
    []int{100, 200, 300, 400},
    []int{150, 250, 350, 450},
    []byte{})
  rQuery := NewGRanges(
    []string{"chr1", "chr4", "chr4", "chr4", "chr4", "chr4"},
    []int{100, 110, 190, 340, 390, 450},
    []int{150, 120, 220, 360, 400, 500},
    []byte{})

  queryHits, subjectHits := FindOverlaps(rQuery, rSubjects)

  queryHits: [1 2 3 4 5]
subjectHits: [0 1 2 3 3]

Genes

Download gene list from UCSC and export it to file:

  genes := ImportGenesFromUCSC("hg19", "ensGene")
  genes.WriteTable("hg19.knownGene.txt", true, false)
  fmt.Println(genes)

                 names seqnames          transcripts                  cds strand
     1 ENST00000456328     chr1 [   11868,    14409) [   14409,    14409)      +
     2 ENST00000515242     chr1 [   11871,    14412) [   14412,    14412)      +
     3 ENST00000518655     chr1 [   11873,    14409) [   14409,    14409)      +
     4 ENST00000450305     chr1 [   12009,    13670) [   13670,    13670)      +
     5 ENST00000423562     chr1 [   14362,    29370) [   29370,    29370)      -
                   ...      ...                  ...                  ...       
204936 ENST00000420810     chrY [28695571, 28695890) [28695890, 28695890)      +
204937 ENST00000456738     chrY [28732788, 28737748) [28737748, 28737748)      -
204938 ENST00000435945     chrY [28740997, 28780799) [28780799, 28780799)      -
204939 ENST00000435741     chrY [28772666, 28773306) [28773306, 28773306)      -
204940 ENST00000431853     chrY [59001390, 59001635) [59001635, 59001635)      +

Import expression data from a GTF file:

  genes.ImportGTF("genesExpr_test.gtf.gz", "transcript_id", "FPKM", false)

                 names seqnames          transcripts                  cds strand |          expr
     1 ENST00000456328     chr1 [   11868,    14409) [   14409,    14409)      + |      0.073685
     2 ENST00000515242     chr1 [   11871,    14412) [   14412,    14412)      + |      0.000000
     3 ENST00000518655     chr1 [   11873,    14409) [   14409,    14409)      + |      0.000000
     4 ENST00000450305     chr1 [   12009,    13670) [   13670,    13670)      + |      0.000000
     5 ENST00000423562     chr1 [   14362,    29370) [   29370,    29370)      - |     10.413931
                   ...      ...                  ...                  ...        |           ...
204936 ENST00000420810     chrY [28695571, 28695890) [28695890, 28695890)      + |      0.000000
204937 ENST00000456738     chrY [28732788, 28737748) [28737748, 28737748)      - |      0.000000
204938 ENST00000435945     chrY [28740997, 28780799) [28780799, 28780799)      - |      0.000000
204939 ENST00000435741     chrY [28772666, 28773306) [28773306, 28773306)      - |      0.000000
204940 ENST00000431853     chrY [59001390, 59001635) [59001635, 59001635)      + |      0.000000

Peaks

Import peaks from a MACS xls file:

  peaks := ImportXlsPeaks("peaks_test.xls")

   seqnames             ranges strand |  abs_summit     pileup -log10(pvalue) fold_enrichment -log10(qvalue)
 1       2L [   5757,    6001)      * |        5865  33.000000      19.809300        6.851880      17.722200
 2       2L [  47233,   47441)      * |       47354  36.000000      19.648200        6.263150      17.566200
 3       2L [  66379,   67591)      * |       66957 252.000000     350.151250       50.986050     346.525450
 4       2L [  72305,   72838)      * |       72525 170.000000     208.558240       34.460930     205.734390
 5       2L [  72999,   73218)      * |       73130  25.000000      12.711700        5.239670      10.700880
        ...                ...        |         ...        ...            ...             ...            ...
12       2R [3646319, 3646794)      * |     3646442  37.000000      23.176910        7.455710      21.063850
13       2R [3666770, 3668041)      * |     3667119 215.000000     279.229060       41.551060     276.108090
14       2R [3668231, 3668441)      * |     3668363  22.000000       9.943110        4.476950       7.976070
15       2R [3670063, 3670393)      * |     3670180  38.000000      19.474590        5.901360      17.393440
16       2R [3670470, 3670927)      * |     3670719 227.000000     305.243350       45.831180     301.974760

Track

Import ChIP-seq reads from bed files and create a track with the normalized signal:

  fmt.Fprintf(os.Stderr, "Parsing reads (treatment) ...\n")
  treatment1 := GRanges{}
  treatment1.ImportBed6("SRR094207.bed")
  treatment2 := GRanges{}
  treatment2.ImportBed6("SRR094208.bed")
  fmt.Fprintf(os.Stderr, "Parsing reads (control)   ...\n")
  control1   := GRanges{}
  control1.ImportBed6("SRR094215.bed")
  control2   := GRanges{}
  control2.ImportBed6("SRR094216.bed")

  genome  := Genome{}
  genome.Import("Data/hg19.genome")
  d       := 200 // d=200 (see *_peaks.xls)
  binsize := 100 // binsize of the track
  pcounts := 1   // pseudocounts
  track := NormalizedTrack("H3K4me3",
    []GRanges{treatment1, treatment2}, []GRanges{control1, control2},
    genome, d, binsize, pcounts, pcounts, false)

Export track to wig or bigWig:

  track.WriteWiggle("track.wig", "track description")
  track.WriteBigWig("track.bw",  "track description")

BigWig Files

BigWig files contain data in a binary format optimized for fast random access. In addition to the raw data, bigWig files typically contain several zoom levels for which the data has been summarized. The BigWigReader class allows to query data and it automatically selects an appropriate zoom level for the given binsize:

  reader, err := NewBigWigReader("test.bw")
  if err != nil {
    log.Fatal(err)
  }
  // query details
  seqname := "chr4" // (regular expression)
  from    := 11774000
  to      := 11778000
  binsize := 20

  for record := range reader.Query(seqname, from, to, binsize) {
    if record.Error != nil {
      log.Fatalf("reading bigWig failed: %v", record.Error)
    }
    fmt.Println(record)
  }

Documentation

Index

Constants

View Source 
const BIGWIG_MAGIC = 0x888FFC26
View Source 
const BbiMaxZoomLevels = 10 /* Max number of zoom levels */
View Source 
const BbiResIncrement = 4 /* Amount to reduce at each zoom level */
View Source 
const BbiTypeBedGraph = 1
View Source 
const BbiTypeFixed = 3
View Source 
const BbiTypeVariable = 2
View Source 
const CIRTREE_MAGIC = 0x78ca8c91
View Source 
const IDX_MAGIC = 0x2468ace0

Variables

View Source 
var ErrFraglenEstimate = fmt.Errorf("estimating fragment length failed")

Functions

func BinDiscreteMax 

func BinDiscreteMax(sum, sumSquares, min, max, n float64) float64

func BinDiscreteMean 

func BinDiscreteMean(sum, sumSquares, min, max, n float64) float64

func BinDiscreteMin 

func BinDiscreteMin(sum, sumSquares, min, max, n float64) float64

func BinMax 

func BinMax(sum, sumSquares, min, max, n float64) float64

func BinMean 

func BinMean(sum, sumSquares, min, max, n float64) float64

func BinMin 

func BinMin(sum, sumSquares, min, max, n float64) float64

func BinVariance 

func BinVariance(sum, sumSquares, min, max, n float64) float64

func CrosscorrelateReads 

func CrosscorrelateReads(reads ReadChannel, genome Genome, maxDelay, binSize int) ([]int, []float64, int, uint64, error)

Compute crosscorrelation between reads on the forward and reverse strand.

func EstimateFragmentLength 

func EstimateFragmentLength(reads ReadChannel, genome Genome, maxDelay, binSize int, fraglenRange [2]int) (int, []int, []float64, uint64, error)

func FindNearest 

func FindNearest(query, subject GRanges, k int) ([]int, []int, []int)

For every query region find the k nearest subject regions including all overlapping regions.

func FindOverlaps 

func FindOverlaps(query, subject GRanges) ([]int, []int)

func IsBamFile 

func IsBamFile(filename string) (bool, error)

func IsBigWigFile 

func IsBigWigFile(filename string) (bool, error)

func NewEndPointList 

func NewEndPointList() endPointList

func ObservedOverExpectedCpG 

func ObservedOverExpectedCpG(sequence []byte) float64

Gardiner-Garden and Frommer, J. Mol. Biol. (1987) 196 (2), 261-282: 

observed * length / (number of C * number of G)

func ParseCigar 

func ParseCigar(cigar BamCigar) <-chan CigarBlock

func TrackAutocorrelation 

func TrackAutocorrelation(track Track, from, to int, normalize bool) (x []int, y []float64, err error)

Compute the sample autocorrelation. If [normalize] is true the result is normalized by mean and variance. The arguments [from] and [to] specify the range of the delay in basepairs.

func TrackCrosscorrelation 

func TrackCrosscorrelation(track1, track2 Track, from, to int, normalize bool) (x []int, y []float64, err error)

Compute the sample cross-correlation between track1 and track2. If [normalize] is true the result is normalized by mean and variance. The arguments [from] and [to] specify the range of the delay in basepairs.

Types

type Alphabet 

type Alphabet interface {
	Bases(i byte) ([]byte, error)
	Matching(i byte) ([]byte, error)
	Code(i byte) (byte, error)
	Decode(i byte) (byte, error)
	IsAmbiguous(i byte) (bool, error)
	IsWildcard(i byte) (bool, error)
	Length() int
	LengthUnambiguous() int
	String() string
}

type AmbiguousNucleotideAlphabet 

type AmbiguousNucleotideAlphabet struct {
}

func (AmbiguousNucleotideAlphabet) Bases 

func (AmbiguousNucleotideAlphabet) Bases(i byte) ([]byte, error)

func (AmbiguousNucleotideAlphabet) Code 

func (AmbiguousNucleotideAlphabet) Code(i byte) (byte, error)

func (AmbiguousNucleotideAlphabet) Complement 

func (AmbiguousNucleotideAlphabet) Complement(i byte) (byte, error)

func (AmbiguousNucleotideAlphabet) ComplementCoded 

func (AmbiguousNucleotideAlphabet) ComplementCoded(i byte) (byte, error)

func (AmbiguousNucleotideAlphabet) Decode 

func (AmbiguousNucleotideAlphabet) Decode(i byte) (byte, error)

func (AmbiguousNucleotideAlphabet) IsAmbiguous 

func (AmbiguousNucleotideAlphabet) IsAmbiguous(i byte) (bool, error)

func (AmbiguousNucleotideAlphabet) IsWildcard 

func (AmbiguousNucleotideAlphabet) IsWildcard(i byte) (bool, error)

func (AmbiguousNucleotideAlphabet) Length 

func (AmbiguousNucleotideAlphabet) Length() int

func (AmbiguousNucleotideAlphabet) LengthUnambiguous 

func (AmbiguousNucleotideAlphabet) LengthUnambiguous() int

func (AmbiguousNucleotideAlphabet) Matching 

func (AmbiguousNucleotideAlphabet) Matching(i byte) ([]byte, error)

func (AmbiguousNucleotideAlphabet) String 

func (AmbiguousNucleotideAlphabet) String() string

type BData 

type BData struct {
	KeySize       uint32
	ValueSize     uint32
	ItemsPerBlock uint32
	ItemCount     uint64

	Keys   [][]byte
	Values [][]byte

	PtrKeys   []int64
	PtrValues []int64
}

func NewBData 

func NewBData() *BData

func (*BData) Add 

func (data *BData) Add(key, value []byte) error

func (*BData) Read 

func (data *BData) Read(file io.ReadSeeker, order binary.ByteOrder) error

func (*BData) Write 

func (data *BData) Write(file io.WriteSeeker, order binary.ByteOrder) error

type BTree 

type BTree struct {
	KeySize       uint32
	ValueSize     uint32
	ItemsPerBlock uint32
	ItemCount     uint64
	Root          BVertex
}

func NewBTree 

func NewBTree(data *BData) *BTree

func (*BTree) Write 

func (tree *BTree) Write(file io.WriteSeeker, order binary.ByteOrder) error

type BVertex 

type BVertex struct {
	IsLeaf   uint8
	Keys     [][]byte
	Values   [][]byte
	Children []BVertex
}

func (*BVertex) BuildTree 

func (vertex *BVertex) BuildTree(data *BData, from, to uint64, level int) (uint64, error)

type BamAuxiliary 

type BamAuxiliary struct {
	Tag   [2]byte
	Value interface{}
}

func (*BamAuxiliary) Read 

func (aux *BamAuxiliary) Read(reader io.Reader) (int, error)

func (*BamAuxiliary) String 

func (aux *BamAuxiliary) String() string

type BamBlock 

type BamBlock struct {
	RefID        int32
	Position     int32
	Bin          uint16
	MapQ         uint8
	RNLength     uint8
	Flag         BamFlag
	NCigarOp     uint16
	LSeq         int32
	NextRefID    int32
	NextPosition int32
	TLength      int32
	ReadName     string
	Cigar        BamCigar
	Seq          BamSeq
	Qual         BamQual
	Auxiliary    []BamAuxiliary
}

type BamCigar 

type BamCigar []uint32

func (BamCigar) AlignmentLength 

func (cigar BamCigar) AlignmentLength() int

func (BamCigar) String 

func (cigar BamCigar) String() string

type BamCoverageConfig 

type BamCoverageConfig struct {
	Logger                  *log.Logger
	BinningMethod           string
	BinSize                 int
	BinOverlap              int
	NormalizeTrack          string
	ShiftReads              [2]int
	PairedAsSingleEnd       bool
	PairedEndStrandSpecific bool
	LogScale                bool
	Pseudocounts            [2]float64
	EstimateFraglen         bool
	FraglenRange            [2]int
	FraglenBinSize          int
	FilterChroms            []string
	FilterMapQ              int
	FilterReadLengths       [2]int
	FilterDuplicates        bool
	FilterStrand            byte
	FilterPairedEnd         bool
	FilterSingleEnd         bool
	SmoothenControl         bool
	SmoothenSizes           []int
	SmoothenMin             float64
}

func BamCoverageDefaultConfig 

func BamCoverageDefaultConfig() BamCoverageConfig

type BamFile 

type BamFile struct {
	BamReader
	// contains filtered or unexported fields
}

func OpenBamFile 

func OpenBamFile(filename string, args ...interface{}) (*BamFile, error)

func (*BamFile) Close 

func (obj *BamFile) Close() error

type BamFlag 

type BamFlag uint16

func (BamFlag) Bit 

func (flag BamFlag) Bit(i uint) bool

func (BamFlag) Duplicate 

func (flag BamFlag) Duplicate() bool

func (BamFlag) FirstInPair 

func (flag BamFlag) FirstInPair() bool

func (BamFlag) MateReverseStrand 

func (flag BamFlag) MateReverseStrand() bool

func (BamFlag) MateUnmapped 

func (flag BamFlag) MateUnmapped() bool

func (BamFlag) NotPassingFilters 

func (flag BamFlag) NotPassingFilters() bool

func (BamFlag) ReadMappedProperPaired 

func (flag BamFlag) ReadMappedProperPaired() bool

func (BamFlag) ReadPaired 

func (flag BamFlag) ReadPaired() bool

func (BamFlag) ReverseStrand 

func (flag BamFlag) ReverseStrand() bool

func (BamFlag) SecondInPair 

func (flag BamFlag) SecondInPair() bool

func (BamFlag) SecondaryAlignment 

func (flag BamFlag) SecondaryAlignment() bool

func (BamFlag) Unmapped 

func (flag BamFlag) Unmapped() bool

type BamHeader 

type BamHeader struct {
	TextLength int32
	Text       string
	NRef       int32
}

type BamQual 

type BamQual []byte

func (BamQual) String 

func (qual BamQual) String() string

type BamReader 

type BamReader struct {
	BgzfReader
	Options BamReaderOptions
	Header  BamHeader
	Genome  Genome
}

func NewBamReader 

func NewBamReader(r io.Reader, args ...interface{}) (*BamReader, error)

func (*BamReader) Read 

func (reader *BamReader) Read() <-chan *BamReaderType2

Read single or paired end reads

func (*BamReader) ReadPairedEnd 

func (reader *BamReader) ReadPairedEnd() <-chan *BamReaderType2

func (*BamReader) ReadSimple 

func (reader *BamReader) ReadSimple(joinPairs, pairedEndStrandSpecific bool) ReadChannel

Simplified reader of single and paired-end reads. All reads that are not mapped are dropped. For paired end reads, if [joinPairs] is true then the range gives the position and length of the entire fragment. If any of the two reads is marked as duplicate, then the result is marked as duplicate. The mapping quality of the result is the minimum quality of the two reads. Any paired end reads that are not properly paired are ignored

func (*BamReader) ReadSingleEnd 

func (reader *BamReader) ReadSingleEnd() <-chan *BamReaderType1

type BamReaderOptions 

type BamReaderOptions struct {
	ReadName      bool
	ReadCigar     bool
	ReadSequence  bool
	ReadAuxiliary bool
	ReadQual      bool
}

type BamReaderType1 

type BamReaderType1 struct {
	BamBlock
	Error error
}

type BamReaderType2 

type BamReaderType2 struct {
	Block1 BamBlock
	Block2 BamBlock
	Error  error
}

type BamSeq 

type BamSeq []byte

func (BamSeq) String 

func (seq BamSeq) String() string

type BbiBlockDecoder 

type BbiBlockDecoder interface {
	Decode() BbiBlockDecoderIterator
}

type BbiBlockDecoderIterator 

type BbiBlockDecoderIterator interface {
	Get() *BbiBlockDecoderType
	Ok() bool
	Next()
}

type BbiBlockDecoderType 

type BbiBlockDecoderType struct {
	BbiSummaryRecord
}

type BbiBlockEncoder 

type BbiBlockEncoder interface {
	Encode(chromid int, sequence []float64, binSize int) BbiBlockEncoderIterator
}

type BbiBlockEncoderIterator 

type BbiBlockEncoderIterator interface {
	Get() *BbiBlockEncoderType
	Ok() bool
	Next()
}

type BbiBlockEncoderType 

type BbiBlockEncoderType struct {
	From  int
	To    int
	Block []byte
}

type BbiDataHeader 

type BbiDataHeader struct {
	ChromId   uint32
	Start     uint32
	End       uint32
	Step      uint32
	Span      uint32
	Type      byte
	Reserved  byte
	ItemCount uint16
}

func (*BbiDataHeader) ReadBuffer 

func (header *BbiDataHeader) ReadBuffer(buffer []byte, order binary.ByteOrder)

func (*BbiDataHeader) WriteBuffer 

func (header *BbiDataHeader) WriteBuffer(buffer []byte, order binary.ByteOrder)

type BbiFile 

type BbiFile struct {
	Header    BbiHeader
	ChromData BData
	Index     RTree
	IndexZoom []RTree
	Order     binary.ByteOrder
}

func NewBbiFile 

func NewBbiFile() *BbiFile

func (*BbiFile) Create 

func (bwf *BbiFile) Create(writer io.WriteSeeker) error

func (*BbiFile) Open 

func (bwf *BbiFile) Open(reader_ io.ReadSeeker) error

func (*BbiFile) Query 

func (bwf *BbiFile) Query(reader io.ReadSeeker, chromId, from, to, binSize int) <-chan BbiQueryType

func (*BbiFile) ReadIndex 

func (bwf *BbiFile) ReadIndex(reader_ io.ReadSeeker) error

func (*BbiFile) ReadZoomIndex 

func (bwf *BbiFile) ReadZoomIndex(reader_ io.ReadSeeker, i int) error

func (*BbiFile) WriteChromList 

func (bwf *BbiFile) WriteChromList(writer io.WriteSeeker) error

func (*BbiFile) WriteIndex 

func (bwf *BbiFile) WriteIndex(writer io.WriteSeeker) error

func (*BbiFile) WriteIndexZoom 

func (bwf *BbiFile) WriteIndexZoom(writer io.WriteSeeker, i int) error

type BbiHeader 

type BbiHeader struct {
	Magic             uint32
	Version           uint16
	ZoomLevels        uint16
	CtOffset          uint64
	DataOffset        uint64
	IndexOffset       uint64
	FieldCould        uint16
	DefinedFieldCount uint16
	SqlOffset         uint64
	SummaryOffset     uint64
	UncompressBufSize uint32
	ExtensionOffset   uint64
	NBasesCovered     uint64
	MinVal            float64
	MaxVal            float64
	SumData           float64
	SumSquares        float64
	ZoomHeaders       []BbiHeaderZoom
	NBlocks           uint64
	// offset positions
	PtrCtOffset          int64
	PtrDataOffset        int64
	PtrIndexOffset       int64
	PtrSqlOffset         int64
	PtrSummaryOffset     int64
	PtrUncompressBufSize int64
	PtrExtensionOffset   int64
}

func NewBbiHeader 

func NewBbiHeader() *BbiHeader

func (*BbiHeader) Read 

func (header *BbiHeader) Read(file io.ReadSeeker, magic uint32) (binary.ByteOrder, error)

func (*BbiHeader) SummaryAddValue 

func (header *BbiHeader) SummaryAddValue(x float64, n int)

func (*BbiHeader) Write 

func (header *BbiHeader) Write(file io.WriteSeeker, order binary.ByteOrder) error

func (*BbiHeader) WriteNBlocks 

func (header *BbiHeader) WriteNBlocks(file io.WriteSeeker, order binary.ByteOrder) error

func (*BbiHeader) WriteOffsets 

func (header *BbiHeader) WriteOffsets(file io.WriteSeeker, order binary.ByteOrder) error

func (*BbiHeader) WriteSummary 

func (header *BbiHeader) WriteSummary(file io.WriteSeeker, order binary.ByteOrder) error

func (*BbiHeader) WriteUncompressBufSize 

func (header *BbiHeader) WriteUncompressBufSize(file io.WriteSeeker, order binary.ByteOrder) error

type BbiHeaderZoom 

type BbiHeaderZoom struct {
	ReductionLevel uint32
	Reserved       uint32
	DataOffset     uint64
	IndexOffset    uint64
	NBlocks        uint32
	PtrDataOffset  int64
	PtrIndexOffset int64
}

func (*BbiHeaderZoom) Read 

func (zoomHeader *BbiHeaderZoom) Read(file io.ReadSeeker, order binary.ByteOrder) error

func (*BbiHeaderZoom) Write 

func (zoomHeader *BbiHeaderZoom) Write(file io.WriteSeeker, order binary.ByteOrder) error

func (*BbiHeaderZoom) WriteNBlocks 

func (zoomHeader *BbiHeaderZoom) WriteNBlocks(file io.WriteSeeker, order binary.ByteOrder) error

func (*BbiHeaderZoom) WriteOffsets 

func (zoomHeader *BbiHeaderZoom) WriteOffsets(file io.WriteSeeker, order binary.ByteOrder) error

type BbiQueryType 

type BbiQueryType struct {
	BbiSummaryRecord
	DataType byte
	Quit     func()
	Error    error
}

func NewBbiQueryType 

func NewBbiQueryType(quit func()) BbiQueryType

type BbiRawBlockDecoder 

type BbiRawBlockDecoder struct {
	Header BbiDataHeader
	Buffer []byte
	// contains filtered or unexported fields
}

func NewBbiRawBlockDecoder 

func NewBbiRawBlockDecoder(buffer []byte, order binary.ByteOrder) (*BbiRawBlockDecoder, error)

func (*BbiRawBlockDecoder) Decode 

func (reader *BbiRawBlockDecoder) Decode() BbiBlockDecoderIterator

func (*BbiRawBlockDecoder) GetDataType 

func (reader *BbiRawBlockDecoder) GetDataType() byte

type BbiRawBlockDecoderIterator 

type BbiRawBlockDecoderIterator struct {
	*BbiRawBlockDecoder
	// contains filtered or unexported fields
}

func (*BbiRawBlockDecoderIterator) Get 

func (it *BbiRawBlockDecoderIterator) Get() *BbiBlockDecoderType

func (*BbiRawBlockDecoderIterator) Next 

func (it *BbiRawBlockDecoderIterator) Next()

func (*BbiRawBlockDecoderIterator) Ok 

func (it *BbiRawBlockDecoderIterator) Ok() bool

type BbiRawBlockEncoder 

type BbiRawBlockEncoder struct {
	ItemsPerSlot int
	// contains filtered or unexported fields
}

func NewBbiRawBlockEncoder 

func NewBbiRawBlockEncoder(itemsPerSlot int, fixedStep bool, order binary.ByteOrder) (*BbiRawBlockEncoder, error)

func (*BbiRawBlockEncoder) Encode 

func (encoder *BbiRawBlockEncoder) Encode(chromid int, sequence []float64, binSize int) BbiBlockEncoderIterator

type BbiRawBlockEncoderIterator 

type BbiRawBlockEncoderIterator struct {
	*BbiRawBlockEncoder
	// contains filtered or unexported fields
}

func (*BbiRawBlockEncoderIterator) Get 

func (it *BbiRawBlockEncoderIterator) Get() *BbiBlockEncoderType

func (*BbiRawBlockEncoderIterator) Next 

func (it *BbiRawBlockEncoderIterator) Next()

func (*BbiRawBlockEncoderIterator) Ok 

func (it *BbiRawBlockEncoderIterator) Ok() bool

type BbiSummaryRecord 

type BbiSummaryRecord struct {
	ChromId int
	From    int
	To      int
	BbiSummaryStatistics
}

func NewBbiSummaryRecord 

func NewBbiSummaryRecord() BbiSummaryRecord

func (*BbiSummaryRecord) AddRecord 

func (record *BbiSummaryRecord) AddRecord(x BbiSummaryRecord)

func (*BbiSummaryRecord) Reset 

func (record *BbiSummaryRecord) Reset()

type BbiSummaryStatistics 

type BbiSummaryStatistics struct {
	Valid      float64
	Min        float64
	Max        float64
	Sum        float64
	SumSquares float64
}

func (*BbiSummaryStatistics) Add 

func (obj *BbiSummaryStatistics) Add(x BbiSummaryStatistics)

func (*BbiSummaryStatistics) AddValue 

func (obj *BbiSummaryStatistics) AddValue(x float64)

func (*BbiSummaryStatistics) Reset 

func (obj *BbiSummaryStatistics) Reset()

type BbiZoomBlockDecoder 

type BbiZoomBlockDecoder struct {
	Buffer []byte
	// contains filtered or unexported fields
}

func NewBbiZoomBlockDecoder 

func NewBbiZoomBlockDecoder(buffer []byte, order binary.ByteOrder) *BbiZoomBlockDecoder

func (*BbiZoomBlockDecoder) Decode 

func (reader *BbiZoomBlockDecoder) Decode() BbiBlockDecoderIterator

type BbiZoomBlockDecoderIterator 

type BbiZoomBlockDecoderIterator struct {
	*BbiZoomBlockDecoder
	// contains filtered or unexported fields
}

func (*BbiZoomBlockDecoderIterator) Get 

func (it *BbiZoomBlockDecoderIterator) Get() *BbiBlockDecoderType

func (*BbiZoomBlockDecoderIterator) Next 

func (it *BbiZoomBlockDecoderIterator) Next()

func (*BbiZoomBlockDecoderIterator) Ok 

func (it *BbiZoomBlockDecoderIterator) Ok() bool

type BbiZoomBlockEncoder 

type BbiZoomBlockEncoder struct {
	ItemsPerSlot int
	// contains filtered or unexported fields
}

func NewBbiZoomBlockEncoder 

func NewBbiZoomBlockEncoder(itemsPerSlot, reductionLevel int, order binary.ByteOrder) (*BbiZoomBlockEncoder, error)

func (*BbiZoomBlockEncoder) Encode 

func (encoder *BbiZoomBlockEncoder) Encode(chromid int, sequence []float64, binSize int) BbiBlockEncoderIterator

type BbiZoomBlockEncoderIterator 

type BbiZoomBlockEncoderIterator struct {
	*BbiZoomBlockEncoder
	// contains filtered or unexported fields
}

func (*BbiZoomBlockEncoderIterator) Get 

func (it *BbiZoomBlockEncoderIterator) Get() *BbiBlockEncoderType

func (*BbiZoomBlockEncoderIterator) Next 

func (it *BbiZoomBlockEncoderIterator) Next()

func (*BbiZoomBlockEncoderIterator) Ok 

func (it *BbiZoomBlockEncoderIterator) Ok() bool

type BbiZoomBlockEncoderType 

type BbiZoomBlockEncoderType struct {
	From  int
	To    int
	Block []byte
}

type BbiZoomRecord 

type BbiZoomRecord struct {
	ChromId    uint32
	Start      uint32
	End        uint32
	Valid      uint32
	Min        float32
	Max        float32
	Sum        float32
	SumSquares float32
}

func (*BbiZoomRecord) AddValue 

func (record *BbiZoomRecord) AddValue(x float64)

func (*BbiZoomRecord) Read 

func (record *BbiZoomRecord) Read(reader io.Reader, order binary.ByteOrder) error

func (BbiZoomRecord) Write 

func (record BbiZoomRecord) Write(writer io.Writer, order binary.ByteOrder) error

type BgzfExtra 

type BgzfExtra struct {
	SI1   uint8
	SI2   uint8
	SLen  uint16
	BSize uint16
}

type BgzfReader 

type BgzfReader struct {
	gzip.Reader
}

func NewBgzfReader 

func NewBgzfReader(r io.Reader) (*BgzfReader, error)

func (*BgzfReader) GetExtra 

func (reader *BgzfReader) GetExtra() (*BgzfExtra, error)

type BigWigFile 

type BigWigFile struct {
	io.ReadSeeker
	// contains filtered or unexported fields
}

func OpenBigWigFile 

func OpenBigWigFile(filename string) (*BigWigFile, error)

func (*BigWigFile) Close 

func (reader *BigWigFile) Close() error

type BigWigParameters 

type BigWigParameters struct {
	BlockSize       int
	ItemsPerSlot    int
	ReductionLevels []int
}

func DefaultBigWigParameters 

func DefaultBigWigParameters() BigWigParameters

type BigWigReader 

type BigWigReader struct {
	Reader io.ReadSeeker
	Bwf    BbiFile
	Genome Genome
}

func NewBigWigReader 

func NewBigWigReader(reader io.ReadSeeker) (*BigWigReader, error)

func (*BigWigReader) GetBinSize 

func (reader *BigWigReader) GetBinSize() (int, error)

func (*BigWigReader) Query 

func (reader *BigWigReader) Query(seqRegex string, from, to, binSize int) <-chan BbiQueryType

func (*BigWigReader) QuerySequence 

func (reader *BigWigReader) QuerySequence(seqregex string, f BinSummaryStatistics, binSize, binOverlap int, init float64) ([]float64, int, error)

func (*BigWigReader) QuerySlice 

func (reader *BigWigReader) QuerySlice(seqregex string, from, to int, f BinSummaryStatistics, binSize, binOverlap int, init float64) ([]float64, int, error)

func (*BigWigReader) ReadBlocks 

func (reader *BigWigReader) ReadBlocks() <-chan BigWigReaderType

type BigWigReaderType 

type BigWigReaderType struct {
	Block []byte
	Error error
}

type BigWigWriter 

type BigWigWriter struct {
	Writer     io.WriteSeeker
	Bwf        BbiFile
	Genome     Genome
	Parameters BigWigParameters

	Leaves map[int][]*RVertex
	// contains filtered or unexported fields
}

func NewBigWigWriter 

func NewBigWigWriter(writer io.WriteSeeker, genome Genome, parameters BigWigParameters) (*BigWigWriter, error)

func (*BigWigWriter) Close 

func (bww *BigWigWriter) Close() error

func (*BigWigWriter) StartZoomData 

func (bww *BigWigWriter) StartZoomData(i int) error

func (*BigWigWriter) Write 

func (bww *BigWigWriter) Write(seqname string, sequence []float64, binSize int) error

func (*BigWigWriter) WriteIndex 

func (bww *BigWigWriter) WriteIndex() error

func (*BigWigWriter) WriteIndexZoom 

func (bww *BigWigWriter) WriteIndexZoom(i int) error

func (*BigWigWriter) WriteZoom 

func (bww *BigWigWriter) WriteZoom(seqname string, sequence []float64, binSize, reductionLevel, i int) error

type BigWigWriterType 

type BigWigWriterType struct {
	Seqname  string
	Sequence []float64
}

type BinSummaryStatistics 

type BinSummaryStatistics func(sum, sumSquares, min, max, n float64) float64

func BinSummaryStatisticsFromString 

func BinSummaryStatisticsFromString(str string) BinSummaryStatistics

type CigarBlock 

type CigarBlock struct {
	N    int
	Type byte
}

type ComplementableAlphabet 

type ComplementableAlphabet interface {
	Bases(i byte) ([]byte, error)
	Matching(i byte) ([]byte, error)
	Code(i byte) (byte, error)
	Decode(i byte) (byte, error)
	Complement(i byte) (byte, error)
	ComplementCoded(i byte) (byte, error)
	IsAmbiguous(i byte) (bool, error)
	IsWildcard(i byte) (bool, error)
	Length() int
	LengthUnambiguous() int
	String() string
}

type GPeaks 

type GPeaks struct {
	GRanges
}

func ImportXlsPeaks 

func ImportXlsPeaks(filename string) (GPeaks, error)

func NewGPeaks 

func NewGPeaks(seqnames []string, from, to, absSummit []int, pileup, pvalue, foldEnrichment, qvalue []float64) GPeaks

func ReadXlsPeaks 

func ReadXlsPeaks(r io.Reader) (GPeaks, error)

func (GPeaks) AbsSummit 

func (p GPeaks) AbsSummit() []int

func (GPeaks) FoldEnrichment 

func (p GPeaks) FoldEnrichment() []float64

func (GPeaks) Pileup 

func (p GPeaks) Pileup() []float64

func (GPeaks) Pvalue 

func (p GPeaks) Pvalue() []float64

func (GPeaks) Qvalue 

func (p GPeaks) Qvalue() []float64

type GRange 

type GRange struct {
	Seqname string
	Range   Range
	Strand  byte
}

type GRanges 

type GRanges struct {
	Seqnames []string
	Ranges   []Range
	Strand   []byte
	Meta
}

func ImportCpGIslandsFromTable 

func ImportCpGIslandsFromTable(filename string) (GRanges, error)

func ImportCpGIslandsFromUCSC 

func ImportCpGIslandsFromUCSC(genome string) GRanges

func NewEmptyGRanges 

func NewEmptyGRanges(n int) GRanges

func NewGRanges 

func NewGRanges(seqnames []string, from, to []int, strand []byte) GRanges

func Promoters 

func Promoters(genes Genes, offset1, offset2 int) (GRanges, error)

Generate a GRanges object where each range is a window around the transcription start site (TSS) of a gene. The arguments offset1, and offset2 determine the size of the window starting from the TSS in 5' and 3' direction respectively. Genomic bounds are not checked. (This is required by the GRanges ImportTrack() method!)

func RandomGRanges 

func RandomGRanges(n, wsize int, genome Genome, useStrand bool) GRanges

Generate a GRanges object where each genomic range is generated at random. Each chromosome is weighted by its length.

func ReadCpGIslandsFromTable 

func ReadCpGIslandsFromTable(r io.ReadSeeker) (GRanges, error)

func (GRanges) Append 

func (r1 GRanges) Append(r2 GRanges) GRanges

func (GRanges) AsReadChannel 

func (obj GRanges) AsReadChannel() ReadChannel

Convert GRanges object to ReadChannel

func (*GRanges) Clone 

func (r *GRanges) Clone() GRanges

func (GRanges) ExportBed3 

func (granges GRanges) ExportBed3(filename string, compress bool) error

func (GRanges) ExportBed6 

func (granges GRanges) ExportBed6(filename string, compress bool) error

func (GRanges) ExportBed9 

func (granges GRanges) ExportBed9(filename string, compress bool) error

func (GRanges) ExportBedGraph 

func (granges GRanges) ExportBedGraph(filename string, compress bool) error

func (GRanges) ExportGTF 

func (granges GRanges) ExportGTF(filename string) error

func (GRanges) ExportTable 

func (granges GRanges) ExportTable(filename string, header, strand, compress bool, args ...interface{}) error

func (GRanges) FilterGenome 

func (r GRanges) FilterGenome(genome Genome) GRanges

Remove all entries that are not in the given genome.

func (GRanges) FilterStrand 

func (r GRanges) FilterStrand(s byte) GRanges

func (GRanges) Genes 

func (granges GRanges) Genes() Genes

func (*GRanges) ImportBamPairedEnd 

func (granges *GRanges) ImportBamPairedEnd(filename string, args ...interface{}) error

func (*GRanges) ImportBamSingleEnd 

func (granges *GRanges) ImportBamSingleEnd(filename string, args ...interface{}) error

func (*GRanges) ImportBed 

func (g *GRanges) ImportBed(filename string, columns int) error

func (*GRanges) ImportBed3 

func (g *GRanges) ImportBed3(filename string) error

func (*GRanges) ImportBed6 

func (g *GRanges) ImportBed6(filename string) error

func (*GRanges) ImportBed9 

func (g *GRanges) ImportBed9(filename string) error

func (*GRanges) ImportBedGraph 

func (g *GRanges) ImportBedGraph(filename string) error

func (*GRanges) ImportBigWig 

func (r *GRanges) ImportBigWig(filename string, name string, s BinSummaryStatistics, binSize, binOverlap int, init float64, revNegStrand bool) error

func (*GRanges) ImportGTF 

func (granges *GRanges) ImportGTF(filename string, optNames, optTypes []string, optDef []interface{}) error

func (*GRanges) ImportTable 

func (granges *GRanges) ImportTable(filename string, names, types []string) error

func (*GRanges) ImportTableAll 

func (granges *GRanges) ImportTableAll(filename string) error

func (*GRanges) ImportTrack 

func (r *GRanges) ImportTrack(track Track, revNegStrand bool) error

Add data from a track to the GRanges object. The data will be contained in a meta-data column with the same name as the track. It is required that each range has the same length.

func (GRanges) Intersection 

func (r GRanges) Intersection(s GRanges) GRanges

func (GRanges) KeepOverlapsWith 

func (r GRanges) KeepOverlapsWith(subject GRanges) GRanges

func (GRanges) Length 

func (r GRanges) Length() int

func (GRanges) Merge 

func (obj GRanges) Merge(granges ...GRanges) GRanges

func (GRanges) ObservedOverExpectedCpG 

func (regions GRanges) ObservedOverExpectedCpG(genomicSequence StringSet) ([]float64, error)

func (GRanges) PrintPretty 

func (granges GRanges) PrintPretty(n int, args ...interface{}) string

func (GRanges) PrintTable 

func (granges GRanges) PrintTable(header, strand bool, args ...interface{}) string

func (GRanges) RandomPermutation 

func (r GRanges) RandomPermutation() GRanges

func (*GRanges) ReadBamPairedEnd 

func (granges *GRanges) ReadBamPairedEnd(r io.Reader, args ...interface{}) error

func (*GRanges) ReadBamSingleEnd 

func (granges *GRanges) ReadBamSingleEnd(r io.Reader, args ...interface{}) error

func (*GRanges) ReadBed 

func (g *GRanges) ReadBed(reader io.Reader, columns int) error

func (*GRanges) ReadBed3 

func (g *GRanges) ReadBed3(r io.Reader) error

Import GRanges from a Bed file with 3 columns.

func (*GRanges) ReadBed6 

func (g *GRanges) ReadBed6(r io.Reader) error

Import GRanges from a Bed file with 6 columns.

func (*GRanges) ReadBed9 

func (g *GRanges) ReadBed9(r io.Reader) error

func (*GRanges) ReadBedGraph 

func (g *GRanges) ReadBedGraph(r io.Reader) error

func (*GRanges) ReadBigWig 

func (r *GRanges) ReadBigWig(bwr *BigWigReader, name string, f BinSummaryStatistics, binSize, binOverlap int, init float64, revNegStrand bool) error

func (*GRanges) ReadGTF 

func (granges *GRanges) ReadGTF(r io.Reader, optNames, optTypes []string, defaults []interface{}) error

Parse expression data from a GTF file (gene transfer format). The data is added as a meta column named "expr" to the gene list. Parameters: 

geneIdName: Name of the optional field containing the gene id
exprIdName: Name of the optional field containing the expression data
genes: List of query genes

func (*GRanges) ReadTable 

func (granges *GRanges) ReadTable(s io.ReadSeeker, names, types []string) error

func (*GRanges) ReadTableAll 

func (granges *GRanges) ReadTableAll(s io.ReadSeeker) error

func (GRanges) Remove 

func (r GRanges) Remove(indices []int) GRanges

func (GRanges) RemoveOverlapsWith 

func (r GRanges) RemoveOverlapsWith(subject GRanges) GRanges

func (GRanges) Row 

func (r GRanges) Row(i int) GRangesRow

func (GRanges) SetLengths 

func (r GRanges) SetLengths(n int) GRanges

Set length of each range to the given value. Ranges with no strand information are not changed.

func (GRanges) Slice 

func (r GRanges) Slice(ifrom, ito int) GRanges

func (GRanges) Sort 

func (r GRanges) Sort(name string, reverse bool) (GRanges, error)

func (GRanges) String 

func (granges GRanges) String() string

func (GRanges) Subset 

func (r GRanges) Subset(indices []int) GRanges

func (GRanges) WriteBed3 

func (granges GRanges) WriteBed3(w io.Writer) error

Export GRanges object as bed file with three columns.

func (GRanges) WriteBed6 

func (granges GRanges) WriteBed6(w io.Writer) error

func (GRanges) WriteBed9 

func (granges GRanges) WriteBed9(w io.Writer) error

func (GRanges) WriteBedGraph 

func (granges GRanges) WriteBedGraph(w io.Writer) error

func (GRanges) WriteGTF 

func (granges GRanges) WriteGTF(w_ io.Writer) error

Export GRanges as GTF file. Required GTF fields should be provided as meta columns named sources, features, scores, and frames. All other meta columns are exported as optional fields.

func (GRanges) WritePretty 

func (granges GRanges) WritePretty(writer io.Writer, n int, args ...interface{}) error

func (GRanges) WriteTable 

func (granges GRanges) WriteTable(writer io.Writer, header, strand bool, args ...interface{}) error

Export GRanges as a table. The first line contains the header of the table.

type GRangesRow 

type GRangesRow struct {
	GRange
	MetaRow
}

func NewGRangesRow 

func NewGRangesRow(granges GRanges, i int) GRangesRow

func (GRangesRow) String 

func (r GRangesRow) String() string

type GappedNucleotideAlphabet 

type GappedNucleotideAlphabet struct {
}

func (GappedNucleotideAlphabet) Bases 

func (GappedNucleotideAlphabet) Bases(i byte) ([]byte, error)

func (GappedNucleotideAlphabet) Code 

func (GappedNucleotideAlphabet) Code(i byte) (byte, error)

func (GappedNucleotideAlphabet) Complement 

func (GappedNucleotideAlphabet) Complement(i byte) (byte, error)

func (GappedNucleotideAlphabet) ComplementCoded 

func (GappedNucleotideAlphabet) ComplementCoded(i byte) (byte, error)

func (GappedNucleotideAlphabet) Decode 

func (GappedNucleotideAlphabet) Decode(i byte) (byte, error)

func (GappedNucleotideAlphabet) IsAmbiguous 

func (GappedNucleotideAlphabet) IsAmbiguous(i byte) (bool, error)

func (GappedNucleotideAlphabet) IsWildcard 

func (GappedNucleotideAlphabet) IsWildcard(i byte) (bool, error)

func (GappedNucleotideAlphabet) Length 

func (GappedNucleotideAlphabet) Length() int

func (GappedNucleotideAlphabet) LengthUnambiguous 

func (GappedNucleotideAlphabet) LengthUnambiguous() int

func (GappedNucleotideAlphabet) Matching 

func (GappedNucleotideAlphabet) Matching(i byte) ([]byte, error)

func (GappedNucleotideAlphabet) String 

func (GappedNucleotideAlphabet) String() string

type GenericMutableTrack 

type GenericMutableTrack struct {
	MutableTrack
}

func (GenericMutableTrack) AddRead 

func (track GenericMutableTrack) AddRead(read Read, d int) error

Add a single read to the track by incrementing the value of each bin that overlaps with the read. Single end reads are extended in 3' direction to have a length of [d]. This is the same as the macs2 `extsize' parameter. Reads are not extended if [d] is zero. The function returns an error if the read's position is out of range

func (GenericMutableTrack) AddReadMeanOverlap 

func (track GenericMutableTrack) AddReadMeanOverlap(read Read, d int) error

Add a single read to the track by adding the fraction of overlap between the read and each bin. Single end reads are extended in 3' direction to have a length of [d]. This is the same as the macs2 `extsize' parameter. Reads are not extended if [d] is zero. The function returns an error if the read's position is out of range

func (GenericMutableTrack) AddReadOverlap 

func (track GenericMutableTrack) AddReadOverlap(read Read, d int) error

Add a single read to the track by adding the number of overlapping nucleotides between the read and each bin. Single end reads are extended in 3' direction to have a length of [d]. This is the same as the macs2 `extsize' parameter. Reads are not extended if [d] is zero. The function returns an error if the read's position is out of range

func (GenericMutableTrack) AddReads 

func (track GenericMutableTrack) AddReads(reads ReadChannel, d int, method string) int

Add reads to track. All single end reads are extended in 3' direction to have a length of [d]. This is the same as the macs2 `extsize' parameter. Reads are not extended if [d] is zero. If [method] is "default", the value of each bin that overlaps the read is incremented. If [method] is "overlap", each bin that overlaps the read is incremented by the number of overlapping nucleotides. If [method] is "mean overlap", each bin that overlaps the read is incremented by the fraction of overlapping nucleotides within the bin. The function returns an error if the read's position is out of range

func (GenericMutableTrack) ImportSegmentation 

func (track GenericMutableTrack) ImportSegmentation(bedFilename string, defState string) ([]string, error)

func (GenericMutableTrack) Map 

func (track1 GenericMutableTrack) Map(track2 Track, f func(string, int, float64) float64) error

Apply a function f to the sequences of track2. The function is given as arguments the name of the sequence, the position, and the value at that position. The return value is stored in track1 if it is not nil.

func (GenericMutableTrack) MapList 

func (track GenericMutableTrack) MapList(tracks []Track, f func(string, int, ...float64) float64) error

func (GenericMutableTrack) Normalize 

func (track GenericMutableTrack) Normalize(treatment, control Track, c1, c2 float64, logScale bool) error

Combine treatment and control from a ChIP-seq experiment into a single track. At each genomic location, the number of binned reads from the treatment experiment is divided by the number of control reads. To avoid division by zero, a pseudocount is added to both treatment and control. The parameter d determines the extension of reads.

func (GenericMutableTrack) QuantileNormalize 

func (track GenericMutableTrack) QuantileNormalize(trackRef Track) error

Quantile normalize track to reference

func (GenericMutableTrack) QuantileNormalizeToCounts 

func (track GenericMutableTrack) QuantileNormalizeToCounts(x []float64, y []int) error

func (GenericMutableTrack) Smoothen 

func (track GenericMutableTrack) Smoothen(minCounts float64, windowSizes []int) error

Smoothen track data with an adaptive window method. For each region the smallest window size among windowSizes is selected which contains at least minCounts counts. If the minimum number of counts is not reached, the larges window size is selected.

func (GenericMutableTrack) WindowMap 

func (track1 GenericMutableTrack) WindowMap(track2 Track, windowSize int, f func(string, int, ...float64) float64) error

Apply a window function f to the sequences of track2. The function is given as arguments the name of the sequence, the position, and the value at that position. The return value is stored in track1 if it is not nil.

func (GenericMutableTrack) WindowMapList 

func (track GenericMutableTrack) WindowMapList(tracks []Track, windowSize int, f func(string, int, ...[]float64) float64) error

type GenericTrack 

type GenericTrack struct {
	Track
}

func (GenericTrack) CumulativeHistogram 

func (track GenericTrack) CumulativeHistogram(from, to float64, bins int) TrackHistogram

func (GenericTrack) ExportBed 

func (track GenericTrack) ExportBed(filename string, compress bool) error

func (GenericTrack) ExportBigWig 

func (track GenericTrack) ExportBigWig(filename string, args ...interface{}) error

func (GenericTrack) ExportSegmentation 

func (track GenericTrack) ExportSegmentation(bedFilename, bedName, bedDescription string, compress bool, stateNames []string, rgbMap map[string]string, scores []Track) error

func (GenericTrack) GRanges 

func (track GenericTrack) GRanges(name string) (GRanges, error)

func (GenericTrack) Histogram 

func (track GenericTrack) Histogram(from, to float64, bins int) TrackHistogram

func (GenericTrack) Reduce 

func (track GenericTrack) Reduce(f func(string, int, float64, float64) float64, x0 float64) map[string]float64

func (GenericTrack) SummaryStatistics 

func (track GenericTrack) SummaryStatistics() TrackSummaryStatistics

func (GenericTrack) WriteBed 

func (track GenericTrack) WriteBed(w io.Writer) error

func (GenericTrack) WriteBigWig 

func (track GenericTrack) WriteBigWig(writer io.WriteSeeker, args ...interface{}) error

type Genes 

type Genes struct {
	GRanges
	// pointer to some meta columns
	Names []string
	Cds   []Range
	// contains filtered or unexported fields
}

Container for genes. Tx contains the transcription start and end positions. Cds specifies the coding regions.

func ImportGenesFromUCSC 

func ImportGenesFromUCSC(genome, table string) (Genes, error)

func NewGenes 

func NewGenes(names, seqnames []string, txFrom, txTo, cdsFrom, cdsTo []int, strand []byte) Genes

func ReadUCSCGenes 

func ReadUCSCGenes(filename string) (Genes, error)

Import genes from UCSC text files. The format is a whitespace separated table with columns: Name, Seqname, TranscriptStart, TranscriptEnd, CodingStart, CodingEnd, and Strand.

func (*Genes) Clone 

func (g *Genes) Clone() Genes

func (Genes) ExportTable 

func (genes Genes) ExportTable(filename string, header, strand, compress bool, args ...interface{}) error

func (Genes) FilterGenome 

func (obj Genes) FilterGenome(genome Genome) Genes

func (Genes) FindGene 

func (g Genes) FindGene(name string) (int, bool)

Returns the index of a gene.

func (*Genes) ImportCufflinksFPKMTracking 

func (genes *Genes) ImportCufflinksFPKMTracking(filename string, verbose bool) error

func (*Genes) ImportGTFExpr 

func (genes *Genes) ImportGTFExpr(filename string, geneIdName, exprIdName string) error

func (Genes) Intersection 

func (obj Genes) Intersection(subject Genes) Genes

func (Genes) KeepOverlapsWith 

func (obj Genes) KeepOverlapsWith(subject Genes) Genes

func (Genes) PrintPretty 

func (genes Genes) PrintPretty(n int) string

func (Genes) PrintTable 

func (genes Genes) PrintTable(header, strand bool, args ...interface{}) string

func (*Genes) ReadCufflinksFPKMTracking 

func (genes *Genes) ReadCufflinksFPKMTracking(r io.Reader, verbose bool) error

Import expression data from cufflinks. The data is added to the gene list as a meta column named "expr".

func (*Genes) ReadGTFExpr 

func (genes *Genes) ReadGTFExpr(r io.Reader, geneIdName, exprIdName string) error

Parse expression data from a GTF file (gene transfer format). The data is added as a meta column named "expr" to the gene list. Parameters: 

geneIdName: Name of the optional field containing the gene id
exprIdName: Name of the optional field containing the expression data
genes: List of query genes

func (Genes) Remove 

func (obj Genes) Remove(indices []int) Genes

func (Genes) RemoveOverlapsWith 

func (obj Genes) RemoveOverlapsWith(subject Genes) Genes

func (Genes) Slice 

func (obj Genes) Slice(ifrom, ito int) Genes

func (Genes) Sort 

func (obj Genes) Sort(name string, reverse bool) (Genes, error)

func (Genes) String 

func (genes Genes) String() string

func (Genes) Subset 

func (obj Genes) Subset(indices []int) Genes

func (Genes) WritePretty 

func (genes Genes) WritePretty(writer io.Writer, n int) error

func (Genes) WriteTable 

func (genes Genes) WriteTable(writer io.Writer, header bool, args ...interface{}) error

type Genome 

type Genome struct {
	Seqnames []string
	Lengths  []int
}

Structure containing chromosome sizes.

func BamImportGenome 

func BamImportGenome(filename string) (Genome, error)

func BamReadGenome 

func BamReadGenome(reader io.Reader) (Genome, error)

func BigWigImportGenome 

func BigWigImportGenome(filename string) (Genome, error)

func BigWigReadGenome 

func BigWigReadGenome(reader io.ReadSeeker) (Genome, error)

func NewGenome 

func NewGenome(seqnames []string, lengths []int) Genome

func (*Genome) AddSequence 

func (genome *Genome) AddSequence(seqname string, length int) (int, error)

func (Genome) Clone 

func (genome Genome) Clone() Genome

func (Genome) Equals 

func (genome Genome) Equals(g Genome) bool

func (Genome) Filter 

func (genome Genome) Filter(f func(name string, length int) bool) Genome

func (Genome) GetIdx 

func (genome Genome) GetIdx(seqname string) (int, error)

func (*Genome) Import 

func (genome *Genome) Import(filename string) error

func (Genome) Length 

func (genome Genome) Length() int

Number of chromosomes in the structure.

func (*Genome) Read 

func (genome *Genome) Read(r io.Reader) error

Import chromosome sizes from a UCSC text file. The format is a whitespace separated table where the first column is the name of the chromosome and the second column the chromosome length.

func (Genome) SeqLength 

func (genome Genome) SeqLength(seqname string) (int, error)

Length of the given chromosome. Returns an error if the chromosome is not found.

func (Genome) String 

func (genome Genome) String() string

func (Genome) SumLengths 

func (genome Genome) SumLengths() int

type GenomeRng 

type GenomeRng struct {
	Weights []float64
	Genome  Genome
	MaxLen  int
}

func NewGenomeRng 

func NewGenomeRng(genome Genome) GenomeRng

func (GenomeRng) Draw 

func (rng GenomeRng) Draw(wsize int) (int, int)

type Kmer 

type Kmer string

func (Kmer) Matches 

func (obj Kmer) Matches(b Kmer, alphabet ComplementableAlphabet) bool

type KmerCatalogue 

type KmerCatalogue struct {
	KmerEquivalenceRelation
	// contains filtered or unexported fields
}

func NewKmerCatalogue 

func NewKmerCatalogue(n, m int, comp, rev, rc bool, maxAmbiguous []int, al ComplementableAlphabet) (*KmerCatalogue, error)

func (*KmerCatalogue) AddKmerClass 

func (obj *KmerCatalogue) AddKmerClass(kmer KmerClass)

func (*KmerCatalogue) CatalogueSize 

func (obj *KmerCatalogue) CatalogueSize() int

func (*KmerCatalogue) Clone 

func (obj *KmerCatalogue) Clone() *KmerCatalogue

func (*KmerCatalogue) GetKmerClass 

func (obj *KmerCatalogue) GetKmerClass(kmer string) KmerClass

func (*KmerCatalogue) GetKmerClassFromId 

func (obj *KmerCatalogue) GetKmerClassFromId(k, id int) KmerClass

func (*KmerCatalogue) GetKmerClassIfPresent 

func (obj *KmerCatalogue) GetKmerClassIfPresent(kmer string) (KmerClass, bool)

type KmerCatalogueIterator 

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

func NewKmerCatalogueIterator 

func NewKmerCatalogueIterator(catalogue KmerCatalogue) KmerCatalogueIterator

func (KmerCatalogueIterator) Get 

func (obj KmerCatalogueIterator) Get() KmerClass

func (*KmerCatalogueIterator) Next 

func (obj *KmerCatalogueIterator) Next()

func (KmerCatalogueIterator) Ok 

func (obj KmerCatalogueIterator) Ok() bool

type KmerClass 

type KmerClass struct {
	KmerClassId
	// list of equivalent K-mers
	Elements []string
}

func NewKmerClass 

func NewKmerClass(k, i int, elements []string) KmerClass

func (KmerClass) CountAmbiguous 

func (obj KmerClass) CountAmbiguous(alphabet ComplementableAlphabet) int

func (KmerClass) CountWildcard 

func (obj KmerClass) CountWildcard(alphabet ComplementableAlphabet) int

func (KmerClass) Equals 

func (obj KmerClass) Equals(b KmerClass) bool

func (KmerClass) Less 

func (obj KmerClass) Less(b KmerClass) bool

func (KmerClass) Matches 

func (obj KmerClass) Matches(b KmerClass, alphabet ComplementableAlphabet) bool

func (KmerClass) String 

func (obj KmerClass) String() string

type KmerClassId 

type KmerClassId struct {
	K int
	I int
}

func (KmerClassId) Equals 

func (a KmerClassId) Equals(b KmerClassId) bool

func (KmerClassId) Less 

func (a KmerClassId) Less(b KmerClassId) bool

type KmerClassList 

type KmerClassList []KmerClass

func (KmerClassList) Clone 

func (obj KmerClassList) Clone() KmerClassList

func (KmerClassList) Equals 

func (obj KmerClassList) Equals(b KmerClassList) bool

func (KmerClassList) Len 

func (obj KmerClassList) Len() int

func (KmerClassList) Less 

func (obj KmerClassList) Less(i, j int) bool

func (KmerClassList) Sort 

func (obj KmerClassList) Sort()

func (KmerClassList) Swap 

func (obj KmerClassList) Swap(i, j int)

func (KmerClassList) Union 

func (obj KmerClassList) Union(b ...KmerClassList) KmerClassList

type KmerClassSet 

type KmerClassSet map[KmerClassId][]string

func (KmerClassSet) AsList 

func (obj KmerClassSet) AsList() KmerClassList

type KmerCounter 

type KmerCounter struct {
	KmerCatalogue
	// contains filtered or unexported fields
}

func NewKmerCounter 

func NewKmerCounter(n, m int, comp, rev, rc bool, maxAmbiguous []int, al ComplementableAlphabet, kmers ...KmerClass) (*KmerCounter, error)

func (*KmerCounter) Clone 

func (obj *KmerCounter) Clone() *KmerCounter

func (*KmerCounter) CountKmers 

func (obj *KmerCounter) CountKmers(sequence []byte) KmerCounts

func (*KmerCounter) Freeze 

func (obj *KmerCounter) Freeze()

func (*KmerCounter) IdentifyKmers 

func (obj *KmerCounter) IdentifyKmers(sequence []byte) KmerCounts

type KmerCounts 

type KmerCounts struct {
	// this is a sorted list of k-mers and might contain more entries than
	// the counts map
	Kmers  KmerClassList
	Counts map[KmerClassId]int
}

func (KmerCounts) At 

func (obj KmerCounts) At(i int) int

func (KmerCounts) GetCount 

func (obj KmerCounts) GetCount(kmer KmerClass) int

func (KmerCounts) GetKmer 

func (obj KmerCounts) GetKmer(i int) KmerClass

func (KmerCounts) Iterate 

func (obj KmerCounts) Iterate() KmerCountsIterator

func (KmerCounts) Len 

func (obj KmerCounts) Len() int

func (KmerCounts) N 

func (obj KmerCounts) N() int

func (*KmerCounts) SetKmers 

func (obj *KmerCounts) SetKmers(kmers KmerClassList)

type KmerCountsIterator 

type KmerCountsIterator struct {
	KmerCounts
	// contains filtered or unexported fields
}

func (KmerCountsIterator) GetCount 

func (obj KmerCountsIterator) GetCount() int

func (KmerCountsIterator) GetIndex 

func (obj KmerCountsIterator) GetIndex() int

func (KmerCountsIterator) GetKmer 

func (obj KmerCountsIterator) GetKmer() KmerClass

func (*KmerCountsIterator) Next 

func (obj *KmerCountsIterator) Next()

func (KmerCountsIterator) Ok 

func (obj KmerCountsIterator) Ok() bool

type KmerCountsList 

type KmerCountsList struct {
	Kmers  KmerClassList
	Counts []map[KmerClassId]int
}

func NewKmerCountsList 

func NewKmerCountsList(counts ...KmerCounts) KmerCountsList

func (KmerCountsList) Append 

func (obj KmerCountsList) Append(args ...KmerCounts) KmerCountsList

func (KmerCountsList) At 

func (obj KmerCountsList) At(i int) KmerCounts

func (KmerCountsList) Len 

func (obj KmerCountsList) Len() int

func (*KmerCountsList) SetKmers 

func (obj *KmerCountsList) SetKmers(kmers KmerClassList)

func (*KmerCountsList) Slice 

func (obj *KmerCountsList) Slice(i, j int) KmerCountsList

type KmerCylinderIterator 

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

func NewKmerCylinderIterator 

func NewKmerCylinderIterator(k int, maxAmbiguous int, alphabet ComplementableAlphabet, j int, a_ string) KmerCylinderIterator

func (KmerCylinderIterator) Get 

func (obj KmerCylinderIterator) Get() string

func (*KmerCylinderIterator) Next 

func (obj *KmerCylinderIterator) Next()

func (KmerCylinderIterator) Ok 

func (obj KmerCylinderIterator) Ok() bool

type KmerEquivalence 

type KmerEquivalence struct {
	N, M         int // min and max kmer size
	Complement   bool
	Reverse      bool
	Revcomp      bool
	MaxAmbiguous []int // maximum number of ambiguous letters
	Alphabet     ComplementableAlphabet
}

func NewKmerEquivalence 

func NewKmerEquivalence(n, m int, comp, rev, rc bool, maxAmbiguous []int, al ComplementableAlphabet) (KmerEquivalence, error)

func (KmerEquivalence) Equals 

func (a KmerEquivalence) Equals(b KmerEquivalence) bool

type KmerEquivalenceRelation 

type KmerEquivalenceRelation struct {
	KmerEquivalence
	// contains filtered or unexported fields
}

func NewKmerEquivalenceRelation 

func NewKmerEquivalenceRelation(n, m int, comp, rev, rc bool, maxAmbiguous []int, al ComplementableAlphabet) (KmerEquivalenceRelation, error)

func (KmerEquivalenceRelation) EquivalenceClass 

func (obj KmerEquivalenceRelation) EquivalenceClass(kmer string) KmerClass

type KmerGraph 

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

func NewKmerGraph 

func NewKmerGraph(kmers KmerClassList, rel KmerEquivalenceRelation) KmerGraph

func NewKmerGraphFromCatalogue 

func NewKmerGraphFromCatalogue(catalogue *KmerCatalogue) KmerGraph

func (KmerGraph) GetNode 

func (obj KmerGraph) GetNode(kmer string) *KmerGraphNode

func (KmerGraph) RelatedKmers 

func (obj KmerGraph) RelatedKmers(kmer string) KmerClassList

type KmerGraphNode 

type KmerGraphNode struct {
	Kmer      KmerClass
	ClusterId uint64
	Rank      int
	// less specific k-mers
	Infra []*KmerGraphNode
	// more specific k-mers
	Supra []*KmerGraphNode
	// k-mers of same length with wildcards at equivalent positions
	Intra []*KmerGraphNode
}

type KmerInstantiationIterator 

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

func NewKmerInstantiationIterator 

func NewKmerInstantiationIterator(alphabet ComplementableAlphabet, a_ string, partial bool) KmerInstantiationIterator

func (KmerInstantiationIterator) Get 

func (obj KmerInstantiationIterator) Get() string

func (*KmerInstantiationIterator) Next 

func (obj *KmerInstantiationIterator) Next()

func (KmerInstantiationIterator) Ok 

func (obj KmerInstantiationIterator) Ok() bool

type KmerIterator 

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

func NewKmerIterator 

func NewKmerIterator(k int, maxAmbiguous int, alphabet ComplementableAlphabet) KmerIterator

func (KmerIterator) Get 

func (obj KmerIterator) Get() string

func (*KmerIterator) Next 

func (obj *KmerIterator) Next()

func (KmerIterator) Ok 

func (obj KmerIterator) Ok() bool

type LazyTrack 

type LazyTrack struct {
	Name       string
	BinSize    int
	BinOverlap int
	Bwr        BigWigReader
	BinSumStat BinSummaryStatistics
	Init       float64
}

func NewLazyTrack 

func NewLazyTrack(reader io.ReadSeeker, name string, f BinSummaryStatistics, binSize, binOverlap int, init float64) (LazyTrack, error)

func (LazyTrack) Clone 

func (track LazyTrack) Clone() LazyTrack

func (LazyTrack) CloneTrack 

func (track LazyTrack) CloneTrack() Track

func (*LazyTrack) FilterGenome 

func (track *LazyTrack) FilterGenome(f func(name string, length int) bool)

func (LazyTrack) GetBinSize 

func (track LazyTrack) GetBinSize() int

func (LazyTrack) GetGenome 

func (track LazyTrack) GetGenome() Genome

func (LazyTrack) GetName 

func (track LazyTrack) GetName() string

func (LazyTrack) GetSeqNames 

func (track LazyTrack) GetSeqNames() []string

func (LazyTrack) GetSequence 

func (track LazyTrack) GetSequence(query string) (TrackSequence, error)

func (LazyTrack) GetSlice 

func (track LazyTrack) GetSlice(r GRangesRow) ([]float64, error)

func (*LazyTrack) ReadBigWig 

func (track *LazyTrack) ReadBigWig(reader io.ReadSeeker, name string, f BinSummaryStatistics, binSize, binOverlap int, init float64) error

type LazyTrackFile 

type LazyTrackFile struct {
	LazyTrack
	// contains filtered or unexported fields
}

func (*LazyTrackFile) Close 

func (obj *LazyTrackFile) Close() error

func (*LazyTrackFile) ImportBigWig 

func (obj *LazyTrackFile) ImportBigWig(filename, name string, s BinSummaryStatistics, binSize, binOverlap int, init float64) error

type Meta 

type Meta struct {
	MetaName []string
	MetaData []interface{}
	// contains filtered or unexported fields
}

func NewMeta 

func NewMeta(names []string, data []interface{}) Meta

func (*Meta) AddMeta 

func (m *Meta) AddMeta(name string, meta interface{})

func (Meta) Append 

func (meta1 Meta) Append(meta2 Meta) Meta

func (*Meta) Clone 

func (m *Meta) Clone() Meta

Deep copy the Meta object.

func (*Meta) DeleteMeta 

func (m *Meta) DeleteMeta(name string)

func (Meta) GetMeta 

func (m Meta) GetMeta(name string) interface{}

func (Meta) GetMetaFloat 

func (m Meta) GetMetaFloat(name string) []float64

func (Meta) GetMetaInt 

func (m Meta) GetMetaInt(name string) []int

func (Meta) GetMetaRange 

func (m Meta) GetMetaRange(name string) []Range

func (Meta) GetMetaStr 

func (m Meta) GetMetaStr(name string) []string

func (Meta) Length 

func (m Meta) Length() int

Returns the number of rows.

func (Meta) Merge 

func (meta Meta) Merge(indices []int) Meta

Return a new Meta object where a given set of rows has been merged. The argument indices should assign the same target index to all rows that should be merged, i.e. indices := []int{0, 1, 1, 2, 3} would merge rows 1 and 2 but leave all rows 0, 3 and 4 as they are. Rows are merged by replacing one-dimensional slices by two-dimensional slices. The Reduce{String,Float64,Int} methods may be used afterwards to apply a function to the merged data. A Meta object that already contains two-dimensional slices cannot be merged.

func (Meta) MetaLength 

func (m Meta) MetaLength() int

Returns the number of columns.

func (*Meta) PrintPretty 

func (meta *Meta) PrintPretty(n int, args ...interface{}) string

func (*Meta) PrintTable 

func (meta *Meta) PrintTable(header bool, args ...interface{}) string

func (*Meta) ReadTable 

func (meta *Meta) ReadTable(r io.Reader, names, types []string) error

func (*Meta) ReduceFloat 

func (meta *Meta) ReduceFloat(name, nameNew string, f func([]float64) float64)

Reduce a column with a two-dimensional float64 slice by applying the given function f. If nameNew != "" the old meta column is kept.

func (*Meta) ReduceInt 

func (meta *Meta) ReduceInt(name, nameNew string, f func([]int) int)

Reduce a column with a two-dimensional int slice by applying the given function f. If nameNew != "" the old meta column is kept.

func (*Meta) ReduceString 

func (meta *Meta) ReduceString(name, nameNew string, f func([]string) string)

Reduce a column with a two-dimensional string slice by applying the given function f. If nameNew != "" the old meta column is kept.

func (Meta) Remove 

func (meta Meta) Remove(indices []int) Meta

func (*Meta) RenameMeta 

func (m *Meta) RenameMeta(nameOld, nameNew string)

func (Meta) Row 

func (m Meta) Row(i int) MetaRow

func (Meta) Slice 

func (meta Meta) Slice(ifrom, ito int) Meta

Return a new Meta object containing rows given by the range [ifrom, ito).

func (*Meta) Sort 

func (meta *Meta) Sort(name string, reverse bool) (Meta, error)

func (*Meta) String 

func (meta *Meta) String() string

func (Meta) Subset 

func (meta Meta) Subset(indices []int) Meta

Return a new Meta object with a subset of the rows from this object.

func (Meta) WritePretty 

func (meta Meta) WritePretty(writer io.Writer, n int, args ...interface{}) error

func (Meta) WriteTable 

func (meta Meta) WriteTable(writer io.Writer, header bool, args ...interface{}) error

type MetaRow 

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

func NewMetaRow 

func NewMetaRow(m Meta, i int) MetaRow

func (MetaRow) GetMeta 

func (m MetaRow) GetMeta(name string) interface{}

func (MetaRow) GetMetaFloat 

func (m MetaRow) GetMetaFloat(name string) (float64, error)

func (MetaRow) GetMetaInt 

func (m MetaRow) GetMetaInt(name string) (int, error)

func (MetaRow) GetMetaStr 

func (m MetaRow) GetMetaStr(name string) (string, error)

type MutableTrack 

type MutableTrack interface {
	Track
	GetMutableSequence(seqname string) (TrackMutableSequence, error)
	CloneMutableTrack() MutableTrack
}

type NucleotideAlphabet 

type NucleotideAlphabet struct {
}

func (NucleotideAlphabet) Bases 

func (NucleotideAlphabet) Bases(i byte) ([]byte, error)

func (NucleotideAlphabet) Code 

func (NucleotideAlphabet) Code(i byte) (byte, error)

func (NucleotideAlphabet) Complement 

func (NucleotideAlphabet) Complement(i byte) (byte, error)

func (NucleotideAlphabet) ComplementCoded 

func (NucleotideAlphabet) ComplementCoded(i byte) (byte, error)

func (NucleotideAlphabet) Decode 

func (NucleotideAlphabet) Decode(i byte) (byte, error)

func (NucleotideAlphabet) IsAmbiguous 

func (NucleotideAlphabet) IsAmbiguous(i byte) (bool, error)

func (NucleotideAlphabet) IsWildcard 

func (NucleotideAlphabet) IsWildcard(i byte) (bool, error)

func (NucleotideAlphabet) Length 

func (NucleotideAlphabet) Length() int

func (NucleotideAlphabet) LengthUnambiguous 

func (NucleotideAlphabet) LengthUnambiguous() int

func (NucleotideAlphabet) Matching 

func (NucleotideAlphabet) Matching(i byte) ([]byte, error)

func (NucleotideAlphabet) String 

func (NucleotideAlphabet) String() string

type OptionBinOverlap 

type OptionBinOverlap struct {
	Value int
}

type OptionBinSize 

type OptionBinSize struct {
	Value int
}

type OptionBinningMethod 

type OptionBinningMethod struct {
	Value string
}

type OptionEstimateFraglen 

type OptionEstimateFraglen struct {
	Value bool
}

type OptionFilterChroms 

type OptionFilterChroms struct {
	Value []string
}

type OptionFilterDuplicates 

type OptionFilterDuplicates struct {
	Value bool
}

type OptionFilterMapQ 

type OptionFilterMapQ struct {
	Value int
}

type OptionFilterPairedEnd 

type OptionFilterPairedEnd struct {
	Value bool
}

type OptionFilterReadLengths 

type OptionFilterReadLengths struct {
	Value [2]int
}

type OptionFilterSingleEnd 

type OptionFilterSingleEnd struct {
	Value bool
}

type OptionFilterStrand 

type OptionFilterStrand struct {
	Value byte
}

type OptionFraglenBinSize 

type OptionFraglenBinSize struct {
	Value int
}

type OptionFraglenRange 

type OptionFraglenRange struct {
	Value [2]int
}

type OptionLogScale 

type OptionLogScale struct {
	Value bool
}

type OptionLogger 

type OptionLogger struct {
	Value *log.Logger
}

type OptionNormalizeTrack 

type OptionNormalizeTrack struct {
	Value string
}

type OptionPairedAsSingleEnd 

type OptionPairedAsSingleEnd struct {
	Value bool
}

type OptionPairedEndStrandSpecific 

type OptionPairedEndStrandSpecific struct {
	Value bool
}

type OptionPrintScientific 

type OptionPrintScientific struct {
	Value bool
}

type OptionPseudocounts 

type OptionPseudocounts struct {
	Value [2]float64
}

type OptionShiftReads 

type OptionShiftReads struct {
	Value [2]int
}

type OptionSmoothenControl 

type OptionSmoothenControl struct {
	Value bool
}

type OptionSmoothenMin 

type OptionSmoothenMin struct {
	Value float64
}

type OptionSmoothenSizes 

type OptionSmoothenSizes struct {
	Value []int
}

type OrderedStringSet 

type OrderedStringSet struct {
	Sequences StringSet
	Seqnames  []string
}

Structure containing genomic sequences.

func EmptyOrderedStringSet 

func EmptyOrderedStringSet() OrderedStringSet

func NewOrderedStringSet 

func NewOrderedStringSet(seqnames []string, sequences [][]byte) OrderedStringSet

func (OrderedStringSet) ExportFasta 

func (obj OrderedStringSet) ExportFasta(filename string, compress bool) error

func (OrderedStringSet) GetSlice 

func (obj OrderedStringSet) GetSlice(name string, r Range) ([]byte, error)

func (*OrderedStringSet) ImportFasta 

func (obj *OrderedStringSet) ImportFasta(filename string) error

func (*OrderedStringSet) ReadFasta 

func (obj *OrderedStringSet) ReadFasta(reader io.Reader) error

func (OrderedStringSet) Scan 

func (obj OrderedStringSet) Scan(query []byte) GRanges

func (OrderedStringSet) WriteFasta 

func (obj OrderedStringSet) WriteFasta(writer io.Writer) error

type PWM 

type PWM struct {
	TFMatrix
}

func (PWM) MaxScore 

func (t PWM) MaxScore(sequence []byte, revcomp bool) float64

Compute the maximum PWM score in the sequence.

func (PWM) MeanScore 

func (t PWM) MeanScore(sequence []byte, revcomp bool) float64

Compute the mean of PWM scores along the sequence.

func (PWM) Scores 

func (t PWM) Scores(sequence []byte, revcomp bool) []float64

Compute the PWM score for every position in the sequence.

type RTree 

type RTree struct {
	BlockSize     uint32
	NItems        uint64
	ChrIdxStart   uint32
	BaseStart     uint32
	ChrIdxEnd     uint32
	BaseEnd       uint32
	IdxSize       uint64
	NItemsPerSlot uint32
	Root          *RVertex
	PtrIdxSize    int64
}

func NewRTree 

func NewRTree() *RTree

func (*RTree) BuildTree 

func (tree *RTree) BuildTree(leaves []*RVertex) error

func (*RTree) IsNil 

func (tree *RTree) IsNil() bool

func (*RTree) Read 

func (tree *RTree) Read(file io.ReadSeeker, order binary.ByteOrder) error

func (*RTree) Write 

func (tree *RTree) Write(file io.WriteSeeker, order binary.ByteOrder) error

func (*RTree) WriteSize 

func (tree *RTree) WriteSize(file io.WriteSeeker, order binary.ByteOrder) error

type RTreeTraverser 

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

func NewRTreeTraverser 

func NewRTreeTraverser(tree *RTree, chromId, from, to int) RTreeTraverser

func (*RTreeTraverser) Get 

func (traverser *RTreeTraverser) Get() *RTreeTraverserType

func (*RTreeTraverser) Next 

func (traverser *RTreeTraverser) Next()

func (*RTreeTraverser) Ok 

func (traverser *RTreeTraverser) Ok() bool

type RTreeTraverserType 

type RTreeTraverserType struct {
	Vertex *RVertex
	Idx    int
}

type RVertex 

type RVertex struct {
	IsLeaf      uint8
	NChildren   uint16
	ChrIdxStart []uint32
	BaseStart   []uint32
	ChrIdxEnd   []uint32
	BaseEnd     []uint32
	DataOffset  []uint64
	Sizes       []uint64
	Children    []*RVertex
	// positions of DataOffset and Sizes values in file
	PtrDataOffset []int64
	PtrSizes      []int64
}

func (*RVertex) Read 

func (vertex *RVertex) Read(file io.ReadSeeker, order binary.ByteOrder) error

func (*RVertex) ReadBlock 

func (vertex *RVertex) ReadBlock(reader io.ReadSeeker, bwf *BbiFile, i int) ([]byte, error)

func (*RVertex) Write 

func (vertex *RVertex) Write(file io.WriteSeeker, order binary.ByteOrder) error

func (*RVertex) WriteBlock 

func (vertex *RVertex) WriteBlock(writer io.WriteSeeker, bwf *BbiFile, i int, block []byte) error

type RVertexGenerator 

type RVertexGenerator struct {
	BlockSize    int
	ItemsPerSlot int
	// contains filtered or unexported fields
}

func NewRVertexGenerator 

func NewRVertexGenerator(blockSize, itemsPerSlot int, order binary.ByteOrder) (*RVertexGenerator, error)

func (*RVertexGenerator) Generate 

func (generator *RVertexGenerator) Generate(idx int, sequence []float64, binSize, reductionLevel int, fixedStep bool) <-chan RVertexGeneratorType

type RVertexGeneratorType 

type RVertexGeneratorType struct {
	Vertex *RVertex
	Blocks [][]byte
}

type RVertexIndexPair 

type RVertexIndexPair struct {
	Vertex *RVertex
	Index  int
}

type RVertexStack 

type RVertexStack []RVertexIndexPair

func (*RVertexStack) Length 

func (stack *RVertexStack) Length() int

func (*RVertexStack) Pop 

func (stack *RVertexStack) Pop() (*RVertex, int)

func (*RVertexStack) Push 

func (stack *RVertexStack) Push(v *RVertex, i int)

type Range 

type Range struct {
	From, To int
}

func NewRange 

func NewRange(from, to int) Range

Range object used to identify a genomic subsequence. By convention the first position in a sequence is numbered 0. The arguments from, to are interpreted as the interval [from, to).

func (Range) Intersection 

func (r Range) Intersection(s Range) Range

func (Range) String 

func (r Range) String() string

type Read 

type Read struct {
	GRange
	MapQ      int
	Duplicate bool
	PairedEnd bool
}

Structure containing information about a read. For paired-end sequencing the range may cover the whole fragment instead of a single read

type ReadChannel 

type ReadChannel <-chan Read

type SimpleTrack 

type SimpleTrack struct {
	Name    string
	Genome  Genome
	Data    TMapType
	BinSize int
}

A track is a container for experimental data mapped to genomic locations. The data is binned in order to reduce memory usage. The first position in a sequence is numbered 0.

func AllocSimpleTrack 

func AllocSimpleTrack(name string, genome Genome, binSize int) SimpleTrack

func BamCoverage 

func BamCoverage(filenameTrack string, filenamesTreatment, filenamesControl []string, fraglenTreatment, fraglenControl []int, options ...interface{}) (SimpleTrack, []fraglenEstimate, []fraglenEstimate, error)

func EmptySimpleTrack 

func EmptySimpleTrack(name string) SimpleTrack

func NewSimpleTrack 

func NewSimpleTrack(name string, sequences [][]float64, genome Genome, binSize int) (SimpleTrack, error)

func (SimpleTrack) Clone 

func (track SimpleTrack) Clone() SimpleTrack

func (SimpleTrack) CloneMutableTrack 

func (track SimpleTrack) CloneMutableTrack() MutableTrack

func (SimpleTrack) CloneTrack 

func (track SimpleTrack) CloneTrack() Track

func (SimpleTrack) ExportBigWig 

func (track SimpleTrack) ExportBigWig(filename string, args ...interface{}) error

func (*SimpleTrack) FilterGenome 

func (track *SimpleTrack) FilterGenome(f func(name string, length int) bool)

func (SimpleTrack) GetBinSize 

func (track SimpleTrack) GetBinSize() int

func (SimpleTrack) GetGenome 

func (track SimpleTrack) GetGenome() Genome

func (SimpleTrack) GetMutableSequence 

func (track SimpleTrack) GetMutableSequence(query string) (TrackMutableSequence, error)

func (SimpleTrack) GetName 

func (track SimpleTrack) GetName() string

func (SimpleTrack) GetSeqNames 

func (track SimpleTrack) GetSeqNames() []string

func (SimpleTrack) GetSequence 

func (track SimpleTrack) GetSequence(query string) (TrackSequence, error)

func (SimpleTrack) GetSlice 

func (track SimpleTrack) GetSlice(r GRangesRow) ([]float64, error)

func (*SimpleTrack) ImportBedGrah 

func (track *SimpleTrack) ImportBedGrah(filename string) error

func (*SimpleTrack) ImportBigWig 

func (track *SimpleTrack) ImportBigWig(filename string, name string, s BinSummaryStatistics, binSize, binOverlap int, init float64) error

func (*SimpleTrack) ImportWiggle 

func (track *SimpleTrack) ImportWiggle(filename string) error

func (SimpleTrack) Index 

func (track SimpleTrack) Index(position int) int

func (*SimpleTrack) ReadBedGraph 

func (track *SimpleTrack) ReadBedGraph(reader io.Reader) error

Import data from wiggle files.

func (*SimpleTrack) ReadBigWig 

func (track *SimpleTrack) ReadBigWig(reader io.ReadSeeker, name string, f BinSummaryStatistics, binSize, binOverlap int, init float64) error

func (*SimpleTrack) ReadWiggle 

func (track *SimpleTrack) ReadWiggle(reader io.Reader) error

Import data from wiggle files.

func (SimpleTrack) ShallowClone 

func (track SimpleTrack) ShallowClone() SimpleTrack

func (SimpleTrack) WriteBigWig 

func (track SimpleTrack) WriteBigWig(writer io.WriteSeeker, args ...interface{}) error

func (SimpleTrack) WriteWiggle 

func (track SimpleTrack) WriteWiggle(filename, description string) error

Export the track to wiggle format. For sparse tracks (more than half of the values are zero), variable step formatting is used.

type StringSet 

type StringSet map[string][]byte

Structure containing genomic sequences.

func EmptyStringSet 

func EmptyStringSet() StringSet

func NewStringSet 

func NewStringSet(seqnames []string, sequences [][]byte) StringSet

func (StringSet) ExportFasta 

func (s StringSet) ExportFasta(filename string, compress bool) error

func (StringSet) GetSlice 

func (s StringSet) GetSlice(name string, r Range) ([]byte, error)

func (StringSet) ImportFasta 

func (s StringSet) ImportFasta(filename string) error

func (StringSet) ReadFasta 

func (s StringSet) ReadFasta(reader io.Reader) error

func (StringSet) Scan 

func (s StringSet) Scan(query []byte) GRanges

func (StringSet) WriteFasta 

func (s StringSet) WriteFasta(writer io.Writer) error

type TFMatrix 

type TFMatrix struct {
	Values [][]float64
}

func EmptyTFMatrix 

func EmptyTFMatrix() TFMatrix

func NewTFMatrix 

func NewTFMatrix(values [][]float64, alphabet Alphabet) TFMatrix

func (TFMatrix) Get 

func (t TFMatrix) Get(c byte, j int) float64

func (TFMatrix) GetRow 

func (t TFMatrix) GetRow(c byte) []float64

func (*TFMatrix) ImportMatrix 

func (t *TFMatrix) ImportMatrix(filename string) error

Read a PWM matrix from file.

func (TFMatrix) Length 

func (t TFMatrix) Length() int

func (*TFMatrix) ReadMatrix 

func (t *TFMatrix) ReadMatrix(reader io.Reader) error

Read a PWM matrix.

func (TFMatrix) RevComp 

func (t TFMatrix) RevComp() TFMatrix

func (TFMatrix) Score 

func (t TFMatrix) Score(sequence []byte, revcomp bool, x0 float64, f func(float64, float64) float64) (float64, error)

Generic function for evaluating a motif on a sequence.

func (*TFMatrix) WriteJaspar 

func (t *TFMatrix) WriteJaspar(writer io.Writer) error

func (*TFMatrix) WriteMatrix 

func (t *TFMatrix) WriteMatrix(writer io.Writer) error

type TMapType 

type TMapType map[string][]float64

type Track 

type Track interface {
	GetName() string
	GetBinSize() int
	GetSequence(seqname string) (TrackSequence, error)
	GetGenome() Genome
	GetSeqNames() []string
	GetSlice(r GRangesRow) ([]float64, error)
	CloneTrack() Track
}

type TrackHistogram 

type TrackHistogram struct {
	Name string
	X    []float64
	Y    []float64
}

func (TrackHistogram) String 

func (histogram TrackHistogram) String() string

type TrackMutableSequence 

type TrackMutableSequence struct {
	TrackSequence
}

type TrackSequence 

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

func (TrackSequence) At 

func (obj TrackSequence) At(i int) float64

func (TrackSequence) AtBin 

func (obj TrackSequence) AtBin(i int) float64

func (TrackSequence) GetBinSize 

func (obj TrackSequence) GetBinSize() int

func (TrackSequence) NBins 

func (obj TrackSequence) NBins() int

func (TrackSequence) Set 

func (obj TrackSequence) Set(i int, v float64)

func (TrackSequence) SetBin 

func (obj TrackSequence) SetBin(i int, v float64)

type TrackSummaryStatistics 

type TrackSummaryStatistics struct {
	Name string
	Mean float64
	Max  float64
	Min  float64
	N    int
}

func (TrackSummaryStatistics) String 

func (statistics TrackSummaryStatistics) String() string

Source Files

View all Source files

Directories

Path Synopsis
lib
bufferedReadSeeker
logarithmetic
progress
seekinghttp
tools
bamCheckBin
bamGenome
bamToBigWig
bamView
bedRemoveOverlaps
bigWigCountsToQuantiles
bigWigEditChromNames
bigWigExtract
bigWigExtractChroms
bigWigGenome
bigWigHistogram
bigWigMap
bigWigNil
bigWigPositive
bigWigQuantileNormalize
bigWigQuery
bigWigQuerySequence
bigWigStatistics
chromHmmTablesToBigWig
countKmers
drawGenomicRegions
fastaExtract
fastaUnresolvedRegions
gtfToBed
memeExtract
observedOverExpectedCpG
pwmScanRegions
pwmScanSequences
segmentationDifferential
sequenceSimilarity

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