transform

Documentation

Overview

Package transform provides functions for transforming sequences.

Index

• func Complement(sequence string) string
• func ComplementBase(basePair rune) rune
• func ComplementBaseRNA(basePair rune) rune
• func ComplementRNA(sequence string) string
• func Reverse(sequence string) string
• func ReverseComplement(sequence string) string
• func ReverseComplementRNA(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/koeng101/dnadesign/lib/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 ComplementBaseRNA

func ComplementBaseRNA(basePair rune) rune

ComplementBaseRNA accepts a RNA 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 ComplementRNA

func ComplementRNA(sequence string) string

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

'A' becomes 'U'
'U' 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.

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/koeng101/dnadesign/lib/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/koeng101/dnadesign/lib/transform"
)

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

}

Output:

TGTAATC

func ReverseComplementRNA

func ReverseComplementRNA(sequence string) string

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

revComplement := Reverse(ComplementRNA(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.