Quick example of using FASTA file to compute consensus strings

consensus_string.go

package main

import (
	"fasta"
	"fmt"
)

func main() {
	fastaFile := fasta.NewFastaFile("cons.txt")

	var dnaLength int

	for _, dna := range fastaFile.DnaSeqs {
		dnaLength = len(dna.Sequence)
		break
	}

	profileMatrix := map[byte][]float64{
		'A': make([]float64, dnaLength),
		'T': make([]float64, dnaLength),
		'C': make([]float64, dnaLength),
		'G': make([]float64, dnaLength),
	}

	for _, dna := range fastaFile.DnaSeqs {
		for index, nucleobase := range dna.Sequence {
			profileMatrix[nucleobase][index] += 1.0
		}
	}

	fmt.Println("A: ", profileMatrix['A'])
	fmt.Println("C: ", profileMatrix['C'])
	fmt.Println("G: ", profileMatrix['G'])
	fmt.Println("T: ", profileMatrix['T'])

	consensusString := make([]byte, dnaLength)

	var (
		dominantKeyAT byte
		dominantKeyGC byte
		dominantKey   byte
	)

	for i, _ := range profileMatrix['A'] {
		if profileMatrix['A'][i] > profileMatrix['T'][i] {
			dominantKeyAT = 'A'
		} else {
			dominantKeyAT = 'T'
		}

		if profileMatrix['G'][i] > profileMatrix['C'][i] {
			dominantKeyGC = 'G'
		} else {
			dominantKeyGC = 'C'
		}

		if profileMatrix[dominantKeyAT][i] > profileMatrix[dominantKeyGC][i] {
			dominantKey = dominantKeyAT
		} else {
			dominantKey = dominantKeyGC
		}

		consensusString[i] = dominantKey
	}

	fmt.Println("Consensus string: ", string(consensusString))
}