Method UpdateWeightsWithSequence

synthesis/codon/codon.go:234–253

UpdateWeightsWithSequence will look at the coding regions in the given genbank data, and use those to generate new weights for the codons in the translation table. The next time a sequence is optimised, it will use those updated weights. This can be used to, for example, figure out which DNA sequen

(data genbank.Genbank)

// This can be used to, for example, figure out which DNA sequence is needed to give the best yield of protein when
// trying to express a protein across different species
func (table *TranslationTable) UpdateWeightsWithSequence(data genbank.Genbank) error {
	codingRegions, err := extractCodingRegion(data)
	if err != nil {
		return err
	}

	table.Stats.GeneCount = len(codingRegions)
	for _, sequence := range codingRegions {
		table.Stats.StartCodonCount[sequence[:3]]++
	}

	if len(codingRegions) == 0 {
		return errNoCodingRegions
	}

	// weight our codon optimization table using the regions we collected from the genbank file above
	newWeights := weightAminoAcids(strings.Join(codingRegions, ""), table.AminoAcids)

	return table.UpdateWeights(newWeights)
}

// Translate will return an amino acid sequence which the given DNA will yield
func (table *TranslationTable) Translate(dnaSeq string) (string, error) {