bed

package

v1.0.1 Latest Latest Go to latest Published: Feb 16, 2017 License: BSD-3-Clause Imports: 14 Imported by: 0

Details

Valid go.mod file
Redistributable license
Tagged version
Stable version
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Repository

github.com/corburn/biogo

Links

Open Source Insights

Documentation ¶

Overview ¶

Package bed provides types to read and write BED format files according to the UCSC specification.

The specification can be found at http://genome.ucsc.edu/FAQ/FAQformat.html#format1.

Index ¶

Variables
type Bed
type Bed3
- func (b *Bed3) Description() string
- func (b *Bed3) End() int
- func (b *Bed3) Format(fs fmt.State, c rune)
- func (b *Bed3) Len() int
- func (b *Bed3) Location() feat.Feature
- func (b *Bed3) Name() string
- func (b *Bed3) Start() int
type Bed4
- func (b *Bed4) Description() string
- func (b *Bed4) End() int
- func (b *Bed4) Format(fs fmt.State, c rune)
- func (b *Bed4) Len() int
- func (b *Bed4) Location() feat.Feature
- func (b *Bed4) Name() string
- func (b *Bed4) Start() int
type Bed5
- func (b *Bed5) Description() string
- func (b *Bed5) End() int
- func (b *Bed5) Format(fs fmt.State, c rune)
- func (b *Bed5) Len() int
- func (b *Bed5) Location() feat.Feature
- func (b *Bed5) Name() string
- func (b *Bed5) Start() int
type Bed6
- func (b *Bed6) Description() string
- func (b *Bed6) End() int
- func (b *Bed6) Format(fs fmt.State, c rune)
- func (b *Bed6) Len() int
- func (b *Bed6) Location() feat.Feature
- func (b *Bed6) Name() string
- func (b *Bed6) Orientation() feat.Orientation
- func (b *Bed6) Start() int
type Bed12
- func (b *Bed12) Description() string
- func (b *Bed12) End() int
- func (b *Bed12) Format(fs fmt.State, c rune)
- func (b *Bed12) Len() int
- func (b *Bed12) Location() feat.Feature
- func (b *Bed12) Name() string
- func (b *Bed12) Orientation() feat.Orientation
- func (b *Bed12) Start() int
type Chrom
- func (c Chrom) Description() string
- func (c Chrom) End() int
- func (c Chrom) Len() int
- func (c Chrom) Location() feat.Feature
- func (c Chrom) Name() string
- func (c Chrom) Start() int
type Reader
- func NewReader(r io.Reader, b int) (*Reader, error)
- func (r *Reader) Line() int
- func (r *Reader) Read() (f feat.Feature, err error)
type Scorer
type Writer
- func NewWriter(w io.Writer, b int) (*Writer, error)
- func (w *Writer) Write(f feat.Feature) (n int, err error)

Constants ¶

This section is empty.

Variables ¶

View Source

var (
	ErrBadBedType         = errors.New("bed: bad bed type")
	ErrBadStrandField     = errors.New("bad strand field")
	ErrBadStrand          = errors.New("invalid strand")
	ErrBadColorField      = errors.New("bad color field")
	ErrMissingBlockValues = errors.New("missing block values")
	ErrNoChromField       = errors.New("no chrom field available")
)

Functions ¶

This section is empty.

Types ¶

type Bed ¶

type Bed interface {
	feat.Feature
	// contains filtered or unexported methods
}

type Bed3 ¶

type Bed3 struct {
	Chrom      string
	ChromStart int
	ChromEnd   int
}

func (*Bed3) Description ¶

func (b *Bed3) Description() string

func (*Bed3) End ¶

func (b *Bed3) End() int

func (*Bed3) Format ¶

func (b *Bed3) Format(fs fmt.State, c rune)

func (*Bed3) Len ¶

func (b *Bed3) Len() int

func (*Bed3) Location ¶

func (b *Bed3) Location() feat.Feature

func (*Bed3) Name ¶

func (b *Bed3) Name() string

func (*Bed3) Start ¶

func (b *Bed3) Start() int

type Bed4 ¶

type Bed4 struct {
	Chrom      string
	ChromStart int
	ChromEnd   int
	FeatName   string
}

func (*Bed4) Description ¶

func (b *Bed4) Description() string

func (*Bed4) End ¶

func (b *Bed4) End() int

func (*Bed4) Format ¶

func (b *Bed4) Format(fs fmt.State, c rune)

func (*Bed4) Len ¶

func (b *Bed4) Len() int

func (*Bed4) Location ¶

func (b *Bed4) Location() feat.Feature

func (*Bed4) Name ¶

func (b *Bed4) Name() string

func (*Bed4) Start ¶

func (b *Bed4) Start() int

type Bed5 ¶

type Bed5 struct {
	Chrom      string
	ChromStart int
	ChromEnd   int
	FeatName   string
	FeatScore  int
}

func (*Bed5) Description ¶

func (b *Bed5) Description() string

func (*Bed5) End ¶

func (b *Bed5) End() int

func (*Bed5) Format ¶

func (b *Bed5) Format(fs fmt.State, c rune)

func (*Bed5) Len ¶

func (b *Bed5) Len() int

func (*Bed5) Location ¶

func (b *Bed5) Location() feat.Feature

func (*Bed5) Name ¶

func (b *Bed5) Name() string

func (*Bed5) Start ¶

func (b *Bed5) Start() int

type Bed6 ¶

type Bed6 struct {
	Chrom      string
	ChromStart int
	ChromEnd   int
	FeatName   string
	FeatScore  int
	FeatStrand seq.Strand
}

func (*Bed6) Description ¶

func (b *Bed6) Description() string

func (*Bed6) End ¶

func (b *Bed6) End() int

func (*Bed6) Format ¶

func (b *Bed6) Format(fs fmt.State, c rune)

func (*Bed6) Len ¶

func (b *Bed6) Len() int

func (*Bed6) Location ¶

func (b *Bed6) Location() feat.Feature

func (*Bed6) Name ¶

func (b *Bed6) Name() string

func (*Bed6) Orientation ¶

func (b *Bed6) Orientation() feat.Orientation

func (*Bed6) Start ¶

func (b *Bed6) Start() int

type Bed12 ¶

type Bed12 struct {
	Chrom       string
	ChromStart  int
	ChromEnd    int
	FeatName    string
	FeatScore   int
	FeatStrand  seq.Strand
	ThickStart  int
	ThickEnd    int
	Rgb         color.RGBA
	BlockCount  int
	BlockSizes  []int
	BlockStarts []int
}

func (*Bed12) Description ¶

func (b *Bed12) Description() string

func (*Bed12) End ¶

func (b *Bed12) End() int

func (*Bed12) Format ¶

func (b *Bed12) Format(fs fmt.State, c rune)

func (*Bed12) Len ¶

func (b *Bed12) Len() int

func (*Bed12) Location ¶

func (b *Bed12) Location() feat.Feature

func (*Bed12) Name ¶

func (b *Bed12) Name() string

func (*Bed12) Orientation ¶

func (b *Bed12) Orientation() feat.Orientation

func (*Bed12) Start ¶

func (b *Bed12) Start() int

type Chrom ¶

type Chrom string

func (Chrom) Description ¶

func (c Chrom) Description() string

func (Chrom) End ¶

func (c Chrom) End() int

func (Chrom) Len ¶

func (c Chrom) Len() int

func (Chrom) Location ¶

func (c Chrom) Location() feat.Feature

func (Chrom) Name ¶

func (c Chrom) Name() string

func (Chrom) Start ¶

func (c Chrom) Start() int

type Reader ¶

type Reader struct {
	BedType int
	// contains filtered or unexported fields
}

BED format reader type.

func NewReader ¶

func NewReader(r io.Reader, b int) (*Reader, error)

Returns a new BED format reader using r.

func (*Reader) Line ¶

func (r *Reader) Line() int

Return the current line number

func (*Reader) Read ¶

func (r *Reader) Read() (f feat.Feature, err error)

Read a single feature and return it or an error.

type Scorer ¶

type Scorer interface {
	Score() int
}

type Writer ¶

type Writer struct {
	BedType int
	// contains filtered or unexported fields
}

BED format writer type.

func NewWriter ¶

func NewWriter(w io.Writer, b int) (*Writer, error)

Returns a new BED format writer using w.

func (*Writer) Write ¶

func (w *Writer) Write(f feat.Feature) (n int, err error)

Write a single feature and return the number of bytes written and any error.

Source Files ¶

View all Source files

bed.go

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