Add NdeI fixing plus regression (#314)

* Add NdeI fixing plus regression

* add comment in code itself

synthesis/fix/synthesis.go

@@ -60,7 +60,14 @@ func RemoveSequence(sequencesToRemove []string, reason string) func(string, chan
 	return func(sequence string, c chan DnaSuggestion, waitgroup *sync.WaitGroup) {
 		var sequencesToRemoveForReverse []string
 		for _, seq := range sequencesToRemove {
-			sequencesToRemoveForReverse = []string{seq, transform.ReverseComplement(seq)}
+			reverseComplementToRemove := transform.ReverseComplement(seq)
+			// Palindromes only have to be fixed once, so add a check here
+			// for palindromes.
+			if reverseComplementToRemove == seq {
+				sequencesToRemoveForReverse = []string{seq}
+			} else {
+				sequencesToRemoveForReverse = []string{seq, reverseComplementToRemove}
+			}
 			for _, site := range sequencesToRemoveForReverse {
 				re := regexp.MustCompile(site)
 				locations := re.FindAllStringIndex(sequence, -1)

synthesis/fix/synthesis_test.go

@@ -216,3 +216,19 @@ func TestPanicIndex(t *testing.T) {
 	_, _, _ = CdsSimple(gene, codonTable, []string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC", "CGTCTC"})
 
 }
+
+func TestNdeIFix(t *testing.T) {
+	// The following used to fail with "Too many fixes required. Number of potential fixes: 0 , number of required fixes: 1"
+	// This was because of an internal NdeI site at a `HM` aa intersection, which is a palindrome.
+	// This would previously cause the palindrome to be found twice, which would add 2 suggested changes
+	// to the change log. Since NdeI cuts at a methionine, only the His can be changed, which is then
+	// frozen. Since the palindrome has two requested fixes, and only 1 can be applied, the problem fails
+	// to fix the sequence. I now added a check if a sequence is a palindrome, and if it is, only search
+	// for a single copy of it.
+	codonTable := codon.ReadCodonJSON(dataDir + "freqB.json")
+	gene := "ATGCGTTTCTTCGAATGCAGCTGCAGCCCGTTCCCGAGCCAGCTGAGCAGCTTTCTGACCCATCTGCTGATCCTGTACACCCTGAGCAGCAGCGTTGAAGCGAGCAGCCGTAATAATTACCAATGGAGCTACGATAGCGATGTCTTTGGTGGCCCGGACTTCTGGGGCCTGGTGGAGAAAGACTGGTGGATGTGCCGTAAAGGTCGTTTGCAAAGCCCGATCGATATTCAACCGGACCGTCTGCTGTTCGATGCGAGCGTCAAACCGGTGCGTCTGGATAAATTGCCGGTGCTGAGCGAATTCGTGAATACCGGCCAGATGGTGCGTATTCGTATTGGTTATAGCACCAAGAAGCCGAGCGTGAACATTACCAACGGTCCGCTGTATGGTTACCGTTACCGTGTTCAGCGCATCGACTTCCATATGGGTCGTGGTAAGGAGAATGGCTCCGAGCATACCATTAACGGCCGCCGCTTTCCGATGGAAGTTCAACTGGTGGCTTTCAATACGGACCTGTATCCGAACTTCACCGCAGCTTCCAAGAGCCCGCACGGCATCGCCATTCTGAGCGTTCTGGTCGATTTCGGTGCACAGACCAACCAGGAGTTGACCAAATTGACCATCGCAACCGCTAGCATCAGCTATAAGGACCAGCGTGTTCAGATGGCCGATTTTGAGCCGTGGCGCTTGTTGCCGTTCACGCGTGACATCATCACCTACGAGGGCAGCCTGACGTCTCCGGGTTGCCACGAGACCGTCACGTGGATCATCCTGAATCAGCCGATCTTCATCACCCGTGAACACTTCGAAGAGTGGAGCCACCTGTACCACACGATGGAAGGCGCAGAGAAAGTCCCGGTGGCCCCGAATTACCGTAAGATTCAGGAGACCAACAATCGCCTGGTGCGCACCAACATTCAGCATAAGGTT"
+	_, _, err := CdsSimple(gene, codonTable, []string{"CTCGAG", "CATATG", "GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC", "CGTCTC"})
+	if err != nil {
+		t.Errorf("Failed to NdeIFix with error: %s", err)
+	}
+}