gtf

Documentation

Overview

Package gtf is used to read gtf features. ref: http://mblab.wustl.edu/GTF22.html

Index

• Constants
• Variables
• type Attribute
• type Feature
  • func ReadFeatures(file string) ([]Feature, error)
  • func ReadFilteredFeatures(file string, chrs []string, feats []string, attrs []string) ([]Feature, error)

Constants

const Version = 2.2

Version is the GTF version

Variables

var Threads = runtime.NumCPU()

Threads for bread.NewBufferedReader()

Types

type Attribute

type Attribute struct {
	Tag, Value string
}

Attribute is the attribute

type Feature

type Feature struct {
	SeqName    string
	Source     string
	Feature    string
	Start      int
	End        int
	Score      *float64
	Strand     *string
	Frame      *int
	Attributes []Attribute
}

Feature is the gff feature struct

func ReadFeatures

func ReadFeatures(file string) ([]Feature, error)

ReadFeatures returns gtf features of a file

func ReadFilteredFeatures

func ReadFilteredFeatures(file string, chrs []string, feats []string, attrs []string) ([]Feature, error)

ReadFilteredFeatures returns gtf features of specific chrs in a file