fasta

Documentation

Index

• func Build(fastas []Fasta) []byte
• func ParseConcurrent(r io.Reader, sequences chan<- Fasta)
• func ReadConcurrent(path string, sequences chan<- Fasta)
• func ReadGzConcurrent(path string, sequences chan<- Fasta)
• func Write(fastas []Fasta, path string)
• type Fasta
  • func Parse(r io.Reader) []Fasta
  • func Read(path string) []Fasta
  • func ReadGz(path string) []Fasta

Examples

• Build
• Parse
• Read
• ReadConcurrent
• ReadGz
• ReadGzConcurrent
• Write

Functions

func Build

func Build(fastas []Fasta) []byte

Build writes a Fasta struct to a string.

Example

ExampleBuild shows basic usage for Build

fastas := Read("data/base.fasta") // get example data
fasta := Build(fastas)            // build a fasta byte array
firstLine := string(bytes.Split(fasta, []byte("\n"))[0])

fmt.Println(firstLine)

Output:

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]

func ParseConcurrent

func ParseConcurrent(r io.Reader, sequences chan<- Fasta)

ParseConcurrent concurrently parses a given Fasta file in an io.Reader into a channel of Fasta structs.

func ReadConcurrent

func ReadConcurrent(path string, sequences chan<- Fasta)

ReadConcurrent concurrently reads a flat Fasta file into a Fasta channel.

Example

ExampleReadConcurrent shows how to use the concurrent parser for decompressed fasta files.

fastas := make(chan Fasta, 100)
go ReadConcurrent("data/base.fasta", fastas)
var name string
for fasta := range fastas {
	name = fasta.Name
}

fmt.Println(name)

Output:

MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken

func ReadGzConcurrent

func ReadGzConcurrent(path string, sequences chan<- Fasta)

ReadGzConcurrent concurrently reads a gzipped Fasta file into a Fasta channel.

Example

ExampleReadGzConcurrent shows how to use the concurrent parser for larger files.

fastas := make(chan Fasta, 1000)
go ReadGzConcurrent("data/uniprot_1mb_test.fasta.gz", fastas)
var name string
for fasta := range fastas {
	name = fasta.Name
}

fmt.Println(name)

Output:

sp|P86857|AGP_MYTCA Alanine and glycine-rich protein (Fragment) OS=Mytilus californianus OX=6549 PE=1 SV=1

func Write

func Write(fastas []Fasta, path string)

Write writes a string to a file.

Example

ExampleWrite shows basic usage of the writer.

fastas := Read("data/base.fasta")       // get example data
Write(fastas, "data/test.fasta")        // write it out again
testSequence := Read("data/test.fasta") // read it in again

os.Remove("data/test.fasta") // getting rid of test file

fmt.Println(testSequence[0].Name)

Output:

gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]

Types

type Fasta

type Fasta struct {
	Name     string `json:"name"`
	Sequence string `json:"sequence"`
}

Fasta is a struct representing a single Fasta file element with a Name and its corresponding Sequence.

func Parse

func Parse(r io.Reader) []Fasta

Parse parses a given Fasta file into an array of Fasta structs. Internally, it uses ParseFastaConcurrent.

Example

ExampleParse shows basic usage for Parse.

file, _ := os.Open("data/base.fasta")
fastas := Parse(file)

fmt.Println(fastas[0].Name)

Output:

gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]

func Read

func Read(path string) []Fasta

Read reads a file into an array of Fasta structs

Example

ExampleRead shows basic usage for Read.

fastas := Read("data/base.fasta")
fmt.Println(fastas[0].Name)

Output:

gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]

func ReadGz

func ReadGz(path string) []Fasta

ReadGz reads a gzipped file into an array of Fasta structs.

Example

ExampleReadGz shows basic usage for ReadGz on a gzip'd file.

fastas := ReadGz("data/uniprot_1mb_test.fasta.gz")
var name string
for _, fasta := range fastas {
	name = fasta.Name
}

fmt.Println(name)

Output:

sp|P86857|AGP_MYTCA Alanine and glycine-rich protein (Fragment) OS=Mytilus californianus OX=6549 PE=1 SV=1