gff

Documentation

Overview

Package gff provides gff parsers and writers.

GFF stands for "general feature format". It is an alternative to GenBank for storing data about genomic sequences. While not often used in synthetic biology research, it is more commonly used in bioinformatics for digesting features of genomic sequences.

This package provides a parser and writer to convert between the gff file format and the more general poly.Sequence struct.

Example (Basic)

This example shows how to open a gff file and search for a gene given its locus tag. We then display the EC number of that particular gene.

package main

import (
	"fmt"
	"github.com/TimothyStiles/poly/io/gff"
)

func main() {
	sequence := gff.Read("../../data/ecoli-mg1655-short.gff")
	for _, feature := range sequence.Features {
		if feature.Attributes["locus_tag"] == "b0003" {
			fmt.Println(feature.Attributes["EC_number"])
		}
	}
}

Output:

2.7.1.39

Index

• func Build(sequence poly.Sequence) []byte
• func Parse(file []byte) poly.Sequence
• func Read(path string) poly.Sequence
• func Write(sequence poly.Sequence, path string)

Examples

• Package (Basic)
• Build
• Parse
• Read
• Write

Functions

func Build

func Build(sequence poly.Sequence) []byte

Build takes an Annotated sequence and returns a byte array representing a gff to be written out.

Example

sequence := Read("../../data/ecoli-mg1655-short.gff")
gffBytes := Build(sequence)
reparsedSequence := Parse(gffBytes)

fmt.Println(reparsedSequence.Meta.Name)

Output:

U00096.3

func Parse

func Parse(file []byte) poly.Sequence

Parse Takes in a string representing a gffv3 file and parses it into an Sequence object.

Example

file, _ := ioutil.ReadFile("../../data/ecoli-mg1655-short.gff")
sequence := Parse(file)

fmt.Println(sequence.Meta.Name)

Output:

U00096.3

func Read

func Read(path string) poly.Sequence

Read takes in a filepath for a .gffv3 file and parses it into an Annotated poly.Sequence struct.

Example

sequence := Read("../../data/ecoli-mg1655-short.gff")
fmt.Println(sequence.Meta.Name)

Output:

U00096.3

func Write

func Write(sequence poly.Sequence, path string)

Write takes an poly.Sequence struct and a path string and writes out a gff to that path.

Example

tmpDataDir, err := ioutil.TempDir("", "data-*")
if err != nil {
	fmt.Println(err.Error())
}
defer os.RemoveAll(tmpDataDir)

sequence := Read("../../data/ecoli-mg1655-short.gff")

tmpGffFilePath := filepath.Join(tmpDataDir, "ecoli-mg1655-short.gff")
Write(sequence, tmpGffFilePath)

testSequence := Read(tmpGffFilePath)

fmt.Println(testSequence.Meta.Name)

Output:

U00096.3