bed2x

package module
v0.0.6 Latest Latest
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 Go to latest Published: Jul 6, 2020 License: BSD-3-Clause Imports: 16 Imported by: 1

README

bed2x

Build Status Releases Go Report Card GoDoc Licenses Linux64 Windows MacOS

Functions

  • get upstream/downstream/intron/exon/promoter/tts/tss/utr3/utr5/cds annotation bed based on input bed12/bed6 bigbed/tabix/gzip/ascii files.
  • fetch cDNA sequence for bed12 format file.
  • support stdin/stdout pipe

Install

Install from go
go get github.com/nimezhu/bed2x/...
Download Binaries

Download pre-compiled files from release.

Usage Examples

bed2x exon [file.bb or file.bed or file.bed.gz]  > file.exon.bed
bed2x promoter file.bb | bed2x seq -g genome.2bit > file.promoter.fa
bed2x read file.bb | head -10 | bed2 seq -g http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit
bed2x read file.bb | head -10 | bed2 seq -g hg19

Documentation

Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func ChromSizes added in v0.0.3 

func ChromSizes(genome string) error

func CigarToCoords added in v0.0.3 

func CigarToCoords(cigar sam.Cigar, offset int) ([]int, []int)

TODO TEST

func IterBed12 

func IterBed12(fn string) (<-chan *Bed12, error)

func IterBed6 

func IterBed6(fn string) (<-chan *Bed6, error)

func IterBedLines 

func IterBedLines(fn string) (<-chan string, error)

IterBedLines: input format could be bigbed,gzip and ascii text file or \S+:\d+-\d+

func RC 

func RC(s string) string

Types

type Bed12 

type Bed12 struct {
	// contains filtered or unexported fields
}

func ParseBed12 

func ParseBed12(line string) (*Bed12, error)

func SamRecordToBed12 added in v0.0.3 

func SamRecordToBed12(s *sam.Record) *Bed12

func (*Bed12) BlockCount 

func (b *Bed12) BlockCount() int

func (*Bed12) BlockSizes 

func (b *Bed12) BlockSizes() []int

func (*Bed12) BlockStarts 

func (b *Bed12) BlockStarts() []int

func (*Bed12) CDS 

func (b *Bed12) CDS() (*Bed12, error)

func (*Bed12) Chr 

func (b *Bed12) Chr() string

func (*Bed12) End 

func (b *Bed12) End() int

func (*Bed12) Exons 

func (b *Bed12) Exons() ([]*Bed6, error)

func (*Bed12) Id 

func (b *Bed12) Id() string

func (*Bed12) Introns 

func (b *Bed12) Introns() ([]*Bed6, error)

func (*Bed12) ItemRgb 

func (b *Bed12) ItemRgb() string

func (*Bed12) Score 

func (b *Bed12) Score() float64

func (*Bed12) Start 

func (b *Bed12) Start() int

func (*Bed12) Strand 

func (b *Bed12) Strand() string

func (*Bed12) String 

func (b *Bed12) String() string

func (*Bed12) ThickEnd 

func (b *Bed12) ThickEnd() int

func (*Bed12) ThickStart 

func (b *Bed12) ThickStart() int

func (*Bed12) UTR3 

func (b *Bed12) UTR3() (*Bed12, error)

func (*Bed12) UTR5 

func (b *Bed12) UTR5() (*Bed12, error)

type Bed3 added in v0.0.3 

type Bed3 interface {
	Chr() string
	Start() int
	End() int
}

type Bed3i 

type Bed3i interface {
	Chr() string
	Start() int
	End() int
}

func ParseRegion added in v0.0.3 

func ParseRegion(s string) (Bed3i, bool)

type Bed4 added in v0.0.3 

type Bed4 struct {
	// contains filtered or unexported fields
}

func (Bed4) Chr added in v0.0.3 

func (b Bed4) Chr() string

func (Bed4) End added in v0.0.3 

func (b Bed4) End() int

func (Bed4) Id added in v0.0.3 

func (b Bed4) Id() string

func (Bed4) Start added in v0.0.3 

func (b Bed4) Start() int

type Bed6 

type Bed6 struct {
	// contains filtered or unexported fields
}

func Downstream 

func Downstream(b Bed6i, bp int) (*Bed6, error)

func ParseBed6 

func ParseBed6(line string) (*Bed6, error)

func Promoter 

func Promoter(b Bed6i, up int, down int) (*Bed6, error)

func Tss 

func Tss(b Bed6i) (*Bed6, error)

func Tts 

func Tts(b Bed6i) (*Bed6, error)

func Upstream 

func Upstream(b Bed6i, bp int) (*Bed6, error)

func (*Bed6) Chr 

func (b *Bed6) Chr() string

func (*Bed6) End 

func (b *Bed6) End() int

func (*Bed6) Exons 

func (b *Bed6) Exons() ([]*Bed6, error)

func (*Bed6) Id 

func (b *Bed6) Id() string

func (*Bed6) Score 

func (b *Bed6) Score() float64

func (*Bed6) Start 

func (b *Bed6) Start() int

func (*Bed6) Strand 

func (b *Bed6) Strand() string

func (*Bed6) String 

func (b *Bed6) String() string

type Bed6i 

type Bed6i interface {
	Bed3i
	Id() string
	Score() float64
	Strand() string
}

type BedI added in v0.0.3 

type BedI interface {
	RangeI
	Chr() string
}

type BinIndex added in v0.0.3 

type BinIndex map[int][]NamedRangeI

type BinIndexMap added in v0.0.3 

type BinIndexMap struct {
	Data map[string]BinIndex
}

func NewBinIndexMap added in v0.0.3 

func NewBinIndexMap() *BinIndexMap

func (*BinIndexMap) Delete added in v0.0.3 

func (d *BinIndexMap) Delete(b NamedBedI) error

TODO Delete

func (*BinIndexMap) Insert added in v0.0.3 

func (c *BinIndexMap) Insert(b NamedBedI) error

func (*BinIndexMap) Load added in v0.0.3 

func (c *BinIndexMap) Load(b []NamedBedI) error

func (*BinIndexMap) Query added in v0.0.3 

func (d *BinIndexMap) Query(b BedI) (<-chan NamedRangeI, error)

func (*BinIndexMap) QueryRegion added in v0.0.3 

func (d *BinIndexMap) QueryRegion(chr string, start int, end int) (<-chan NamedRangeI, error)

type Db added in v0.0.3 

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

func NewDb added in v0.0.3 

func NewDb() Db

func (Db) Get added in v0.0.3 

func (db Db) Get(id string) (Bed6i, error)

* TODO Get All Bed6i with same Id */

func (Db) Load added in v0.0.3 

func (db Db) Load(fn string) error

func (Db) Query added in v0.0.3 

func (db Db) Query(chr string, start int, end int) (<-chan Bed6i, error)

type NamedBedI added in v0.0.3 

type NamedBedI interface {
	BedI
	Id() string
}

type NamedRangeI added in v0.0.3 

type NamedRangeI interface {
	RangeI
	Id() string
}

type RangeI added in v0.0.3 

type RangeI interface {
	Start() int
	End() int
}

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