genome

package

v1.0.4 Latest Latest Go to latest Published: Oct 29, 2021 License: BSD-3-Clause Imports: 2 Imported by: 32

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Repository

github.com/biogo/biogo

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Open Source Insights

Documentation ¶

Overview ¶

Package genome defines types useful for representing cytogenetic features.

Constants ¶

This section is empty.

Variables ¶

This section is empty.

Functions ¶

This section is empty.

Types ¶

type Band ¶

type Band struct {
	Band     string
	Desc     string
	Chr      feat.Feature
	StartPos int
	EndPos   int
	Giemsa   string
}

Band represents a chromosome band.

func (*Band) Description ¶

func (b *Band) Description() string

func (*Band) End ¶

func (b *Band) End() int

func (*Band) Len ¶

func (b *Band) Len() int

func (*Band) Location ¶

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

func (*Band) Name ¶

func (b *Band) Name() string

func (*Band) Start ¶

func (b *Band) Start() int

type Chromosome ¶

type Chromosome struct {
	Chr      string
	Desc     string
	Length   int
	Features []feat.Feature
}

Chromosome represent a chromosome and associated features. Elements in the Features field should return the Chromosome when their Location() method is called.

func (*Chromosome) Description ¶

func (c *Chromosome) Description() string

func (*Chromosome) End ¶

func (c *Chromosome) End() int

func (*Chromosome) Len ¶

func (c *Chromosome) Len() int

func (*Chromosome) Location ¶

func (c *Chromosome) Location() feat.Feature

func (*Chromosome) Name ¶

func (c *Chromosome) Name() string

func (*Chromosome) Start ¶

func (c *Chromosome) Start() int

type Fragment ¶

type Fragment struct {
	Frag      string
	Desc      string
	Chr       feat.Feature
	ChrStart  int
	ChrEnd    int
	FragStart int
	FragEnd   int
	Type      byte
	Strand    seq.Strand
}

Fragment represents an assembly fragment.

func (*Fragment) Description ¶

func (f *Fragment) Description() string

func (*Fragment) End ¶

func (f *Fragment) End() int

func (*Fragment) Len ¶

func (f *Fragment) Len() int

func (*Fragment) Location ¶

func (f *Fragment) Location() feat.Feature

func (*Fragment) Name ¶

func (f *Fragment) Name() string

func (*Fragment) Start ¶

func (f *Fragment) Start() int

Source Files ¶

View all Source files

genome.go

Directories ¶

Path	Synopsis
cow
bt7 Package bt7 defines chromosome and assembly fragment intervals for the bt7 genome assembly for cow.	Package bt7 defines chromosome and assembly fragment intervals for the bt7 genome assembly for cow.
drosophila
dm3 Package dm3 defines chromosome and band intervals for the drosophila karyotype based on the dm3 assembly.	Package dm3 defines chromosome and band intervals for the drosophila karyotype based on the dm3 assembly.
human
hg19 Package hg19 defines chromosome and band intervals for the human karyotype based on the hg19 assembly.	Package hg19 defines chromosome and band intervals for the human karyotype based on the hg19 assembly.
mouse
mm10 Package mm10 defines chromosome and band intervals for the mouse karyotype based on the mm10 assembly.	Package mm10 defines chromosome and band intervals for the mouse karyotype based on the mm10 assembly.

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