transform

Documentation

Overview

Package transform provides functions for transforming sequences.

Index

• func Complement(sequence string) string
• func ComplementBase(basePair rune) rune
• func Reverse(sequence string) string
• func ReverseComplement(sequence string) string

Examples

• Complement
• Reverse
• ReverseComplement

Functions

func Complement

func Complement(sequence string) string

Complement returns the complement of sequence. In DNA each nucleotide (A, T, C or G) is has a deterministic pair. A is paired with T and C is paired with G. The complement of a sequence is formed by exchanging these letters for their pair:

'A' becomes 'T'
'T' becomes 'A'
'C' becomes 'G'
'G' becomes 'C'

This function expects byte characters in the range a-z and A-Z and will not check for non-byte characters, i.e. utf-8 encoding.

Example

package main

import (
	"fmt"

	"github.com/TimothyStiles/poly/transform"
)

func main() {
	sequence := "GATTACA"
	complement := transform.Complement(sequence)
	fmt.Println(complement)

}

Output:

CTAATGT

func ComplementBase

func ComplementBase(basePair rune) rune

ComplementBase accepts a base pair and returns its complement base pair. See Complement.

This function expects byte characters in the range a-z and A-Z and will return a space ' ' (U+0020) for characters that are not matched to any known base. This is subject to change.

func Reverse

func Reverse(sequence string) string

Reverse returns the reverse of sequence. It performs a basic string reversal by working on the bytes.

This function expects byte characters in the range a-z and A-Z and will not check for non-byte character, i.e. utf-8 encoding.

Example

package main

import (
	"fmt"

	"github.com/TimothyStiles/poly/transform"
)

func main() {
	sequence := "GATTACA"
	reverse := transform.Reverse(sequence)
	fmt.Println(reverse)

}

Output:

ACATTAG

func ReverseComplement

func ReverseComplement(sequence string) string

ReverseComplement returns the reversed complement of sequence. It is the equivalent of calling

revComplement := Reverse(Complement(sequence))

This function expects byte characters in the range a-z and A-Z and will not check for non-byte characters, i.e. utf-8 encoding.

Example

package main

import (
	"fmt"

	"github.com/TimothyStiles/poly/transform"
)

func main() {
	sequence := "GATTACA"
	reverseComplement := transform.ReverseComplement(sequence)
	fmt.Println(reverseComplement)

}

Output:

TGTAATC