genome

package
v1.0.3 Latest Latest
Warning

This package is not in the latest version of its module.

Go to latest
Published: Dec 1, 2020 License: BSD-3-Clause Imports: 2 Imported by: 32

Documentation

Overview

Package genome defines types useful for representing cytogenetic features.

Index

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

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.

Jump to

Keyboard shortcuts

? : This menu
/ : Search site
f or F : Jump to
y or Y : Canonical URL