Ensure Non-Met start codons map to Met on translation

Also makes Translate() return an error if an invalid start codon is received

synthesis/codon/codon.go

@@ -87,6 +87,7 @@ type AminoAcid struct {
 type Table interface {
 	Chooser() (map[string]weightedRand.Chooser, error)
 	GenerateTranslationTable() map[string]string
+	GenerateStartCodonTable() map[string]string
 	GetAminoAcids() []AminoAcid
 	GetStartCodons() []string
 	GetStopCodons() []string
@@ -113,15 +114,27 @@ func Translate(sequence string, codonTable Table) (string, error) {
 	var aminoAcids strings.Builder
 	var currentCodon strings.Builder
 	translationTable := codonTable.GenerateTranslationTable()
+	startCodonTable := codonTable.GenerateStartCodonTable()
 
+	startCodonReached := false
 	for _, letter := range sequence {
 
 		// add current nucleotide to currentCodon
 		currentCodon.WriteRune(letter)
 
 		// if current nucleotide is the third in a codon translate to aminoAcid write to aminoAcids and reset currentCodon.
+		// use start codon table for the first codon only, erroring out if an invalid start codon is provided
 		if currentCodon.Len() == 3 {
-			aminoAcids.WriteString(translationTable[strings.ToUpper(currentCodon.String())])
+			if startCodonReached {
+				aminoAcids.WriteString(translationTable[strings.ToUpper(currentCodon.String())])
+			} else {
+				aminoAcid, ok := startCodonTable[strings.ToUpper(currentCodon.String())]
+				if !ok {
+					return "", fmt.Errorf("start codon %q is not in start codon table %v", currentCodon.String(), startCodonTable)
+				}
+				aminoAcids.WriteString(aminoAcid)
+				startCodonReached = true
+			}
 
 			// reset codon string builder for next codon.
 			currentCodon.Reset()
@@ -183,6 +196,17 @@ func (table codonTable) OptimizeTable(sequence string) Table {
 	return table
 }
 
+// GenerateStartCodonTable returns a mapping from the start codons of a Table to their associated amino acids.
+// For our codonTable implementation, assumes that we always map to Met.
+func (table codonTable) GenerateStartCodonTable() map[string]string {
+	result := make(map[string]string)
+	for _, codon := range table.StartCodons {
+		result[codon] = "M"
+	}
+
+	return result
+}
+
 // getCodonFrequency takes a DNA sequence and returns a hashmap of its codons and their frequencies.
 func getCodonFrequency(sequence string) map[string]int {
 

synthesis/codon/codon_test.go

@@ -21,6 +21,26 @@ func TestTranslation(t *testing.T) {
 	}
 
 }
+
+// Non-Met start codons should still map to Met for our standard codon tables.
+// See https://github.com/TimothyStiles/poly/issues/305.
+func TestTranslationAlwaysMapsStartCodonToMet(t *testing.T) {
+	gfpTranslation := "MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK*"
+	gfpDnaSequence := "TTGGCTAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCTACATACGGAAAGCTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCATATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTCGGACACAAACTCGAGTACAACTATAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAACATTGAAGATGGATCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA"
+
+	if got, _ := Translate(gfpDnaSequence, GetCodonTable(11)); got != gfpTranslation {
+		t.Errorf("TestTranslation has failed. Translate has returned %q, want %q", got, gfpTranslation)
+	}
+}
+
+func TestTranslationErrorsOnIncorrectStartCodon(t *testing.T) {
+	badSequence := "GGG"
+
+	if _, gotErr := Translate(badSequence, GetCodonTable(11)); gotErr == nil {
+		t.Errorf("Translation should return an error if given an incorrect start codon")
+	}
+}
+
 func TestTranslationErrorsOnEmptyCodonTable(t *testing.T) {
 	emtpyCodonTable := codonTable{}
 	_, err := Translate("A", emtpyCodonTable)