Fix synthesis buffer problem (#204)

* Fix synthesis buffer problem * Simplify error handling in test functions for complex genes
bebop · Sep 12, 2021 · 3a8faf4 · 3a8faf4
1 parent 86e4812
commit 3a8faf4
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Showing 2 changed files with 12 additions and 4 deletions.
diff --git a/synthesis/synthesis.go b/synthesis/synthesis.go
@@ -143,7 +143,7 @@ func GcContentFixer(upperBound, lowerBound float64) func(string, chan DnaSuggest
 // sequence check and returns a list of all the suggested changes.
 func findProblems(sequence string, problematicSequenceFuncs []func(string, chan DnaSuggestion, *sync.WaitGroup)) []DnaSuggestion {
 	// Run functions to get suggestions
-	suggestions := make(chan DnaSuggestion, 100)
+	suggestions := make(chan DnaSuggestion, 1000000)
 	var waitgroup sync.WaitGroup
 	for _, function := range problematicSequenceFuncs {
 		waitgroup.Add(1)

diff --git a/synthesis/synthesis_test.go b/synthesis/synthesis_test.go
@@ -188,10 +188,18 @@ func TestBtgZIComplexFix(t *testing.T) {
 	complexGene := "ATGAAGCTGATTATTGGCGCAATGCATGAAGAATTGCAGGATTCCATCGCGTTCTATAAGCTGAATAAGGTGGAAAACGAGAAGTTCACCATTTATAAGAATGAAGAGATCATGTTTTGCATTACCGGTATCGGTCTGGTGAACGCGGCGGCGCAGCTGAGCTACATTCTGTCTAAATATGATATTGACTCCATTATTAACATCGGTACCAGCGGCGGTTGCGACAAAGAGCTGAAACAAGGCGACATCCTGATCATCGACAAGATCTATAACAGCGTGGCGGACGCCACCGCATTCGGCTACGCGTACGGCCAAGTTCCGCGTATGCCGAAGTACTATGAAACCAGCAACAAAGATATTATTAAAACCATCAGCAAGGCGAAAATTAAGAATATCGCGAGCTCCGACATCTTCATCCATTCTACGGAGCAAGTGAAGAACTTCATCAATAAAATTGAGGACAAGATTAGCGTCCTGGATATGGAGTGTTTTGCGTATGCTCAGACGGCTTATTTGTTCGAAAAGGAGTTTTCTGTGATTAAAATCATTAGCGACGTCATCGGCGAAAAGAATACCAACAACGTGCAGTTCAACGACTTTATCAAGATTGCCGGTAAGGAGATTTTGGAGATTCTGAAGAAAATTCTG"
 	codonTable := codon.ReadCodonJSON(dataDir + "freqB.json")
 	restrictionEnzymes := []string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}
-	sequence, changes, err := FixCdsSimple(complexGene, codonTable, restrictionEnzymes)
+	_, _, err := FixCdsSimple(complexGene, codonTable, restrictionEnzymes)
+	if err != nil {
+		t.Errorf("Failed to fix complex gene with error: %s", err)
+	}
+}
+
+func TestBufferFailure(t *testing.T) {
+	complexGene := "ATGAAAAAGCTGCTGGCACTGCTGGTTGTGGTCACCTTGACCACCAATGTTGTCGTGGCGGGCGTGGCCATTGCAAACGCGGATAAGAAGAAGCAAAACGACATCCGTATCCTGCAAAGCAAACTGGAGGCAATCCTGAAGAGCAAAACCGATGCGAAGTGGGACGTTTCCGAATTGCAAAAAAAAGTGGATACCGAATTCGGCGAGGGCGAGATTACCGTTAGCTTCAAAGATTATACCAAAGTTACGAGCATTGCAAAGGCTGAATTTATCTTTAAAGCCAACAACAAAAAATACACCGGTCAGCTGACCCTGACCCAGACCTACGAAGTTAAGGATAACAAAGCTGAGGATATCAGCGTCATTAGCACCCGCCTGACGAGCATCCTGAGCGAGAAACCGCACGATGAATGGACCGTTACGGACCTGCAAACCAAGATTGACAGCGAGTTTGGTAATGGTGAGATTGCGGTTAGCGGTGGTACGTATAGCGATGATAACAACTACACCGGCGAAACGAAGAAAAAGGCCGAATTCACGTTCACGGGCAATGCGACCACCGATCCGGAAAACACCCTGAAATACATTGGCGAGATTACGCTGACGCATACGTACACGAAACAAACCGTGATTAGCAACGCTCAGATTAATACGGTGGTGACGGATCTGGCGAATCACGATAAATTCGATAACAAGGAAGCAGCGAAATCCGCGATCGAAGCAGCGTTCGCATACAAGGAGGCGGCAAGCGATGCGGAGCCGACCGGTATCAAGGGTATTGAAAAAGCAGAAGCCAAGTATAACAAGTCCGTGGAAGATGATAAAAGCAGCTTCACCGTGACGTTGACGCTGAGCACGGGTTATGTCCTGGAGCAAACGACCAACACCGTCGAGGTTACGGTGAACTTGATGAGCCGTACCGATATCTCTACCAACGAAGAGTTTAAACAAGAGCTGACCAGCTTTGTGAATGACGAGGCGCACAAGAACCAAGCGTGGACCAAGGACGGTCTGCAAAGCGCGCTGAATACCAAGTATGGCAGCGAGGAGTTTGACGTTACGGAAGACGATAGCACCGTTACGTACGATAATAGCGAACTGGGCAAGAAGACGGAAAAGTTCGTCATCACCGGCCAAGGCAGCAAGGAGAATAATAAACAGTACCAGGGTGAGTTGAAGGTTACGCACGATTACAAGGTTACCGCCAATATTTCTACCATTAAGAACGAGCTGGAGACCATTCTGAAGGATAAAGACTATGAGGAGAAAACGTGGACGCTGGACGAGCTGCAAAAAGCGGTTGATACCGAGTTCAACAAAGGTCAAATTACCGTGGAGGAAGTTATTCTGCTGAAGGATGACAATAGCAATGTGGTTAAAAATACCAAAGAATGGAAATTCATCGGCAATAGCAATGATGAAAACGAATTTGTTTATACCGGTGATGTGACCCTGCCGCACACCTGGAAAAGCTATAAAGTGTTGGCCTCTGATATCCAAACGGCGGCAGAAGTTGCAATTAATGGCAAGAGCTATGCAAATATCGAAGCGGCGCAAGAAGACATCACGAACGCAGTCCAAGCCATCACGGGTGTTGACTCCGTTATTTACCCGACGGAAACGCCGAAAGACTGGAATGATGAAACCATTAAATTTACGGTTACGTTCAAAGAGAACTACGTGATTGAAGGTAAAAATGATTTCAGCGTCAAAGCCCGCGTCGGTAATAGCTCCCAGAATCTGGCGGATATTATTAAGGCGGACGACCTGAAAATCAGCGCGGCAAAAGGCAATGATGCTAGCGCGGTTAAAACCCAAATTGAAACCGTGCTGACCGCTGCGGGTCTGGTGAATGGTACCGATTATGTGGACTTCACCGTGGCGCGTACCGATGATGAGGCTACCACCAGCGTTGAGATCACCGGCAAGGGTAGCGATAAAGTTGTTGATGGTTCCAAAGTTACCTTCGTTGTCACCTGGTCCACCGATTTTTCTAAAGACTTGGCAGACATTATTAAGGCGGACGACCTGAAAATCAGCGCGGCGAAAGGCAATGATGTGAGCACCGTGAAGACCCAAATTGAAACCGTTCTGACGGCTGCGGGTCTGGTGAACGGCACCGACTATGTTGATTTCACCGTCGCGCGTACCGACGATGAAGCGACCACCAGCGTTGAGATTACCGGTAAAGGTAGCGATAAGGTTGTCGACGGCAGCAAGGTTACGTTTGTTGTTACCTGGAGCACCGACTTTAGCAAGGACCTGGCGGACATCATTAAGGCGGACGACTTGAAGATTTCTGCCGCAAAGGGTAATGACGTCAGCACCGTTAAAACCCAAATCGAGACGGTTTTGACCGCAGCGGGTCTGGTGAATGGTACCGATTATGTGGACTTTACGGTGGCACGCACCGACGACGAGGCGACCACCAGCGTGGAAATTACCGGTAAGGGTAGCGACAAGGTTGTTGACGGTAGCAAAGTTACGTTTGTTGTTACGTGGAGCACCGACTTTAGCAAGGATTTGGCAGACATTATCAAAGCCGACGACCTGAAAATTTCTGCGGCCAAGGGCAACGATGTCAGCACCGTTAAGATCCAGATTGAGACCGTGCTGACCGCGGCGGGCCTGGTCAACGGCACCGATTATGTTGATTTCACCGTTGCACGCACCGATGATGAGGCCACGACCAGCGTGGAGATTACCGGTAAGGGTAGCGACAAAGTGGTGGACGGTAGCAAAGTGACCTTCGTTGTGACGTGGAGCATTGATTTCAGCAAAGATCTGGCGGATATTATTAAAGCAGACGACCTGAAGATCTCCGCGGCCAAAGGTAATGATGTTAGCGCGGTCAAGATCCAGATCGAGACGGTTCTGACCGCGGCCGGCTTGGTCAACGGTACGGATTATGTGGACTTCACCGTGGCTCGTACGGATGACGAGGCAACGACCTCTGTGGAGATCACGGGTAAGGGTTCTGATAAGGTTGTCGACGGCAGCAAAGTGACCTTTGTCGTTACCTGGAGCACCGACTTCTCCAAGGACTTGGCAGATATCATTAAGGCCGATGACCTGAAGATCAGCGCTGCGAAAGGTAACGACGTGAGCGCGGTTAAGACCCAAATTGAGACCGTCCTGACCGCAGCGGGCTTGGTTAACGGCACGGATTATGTGGACTTCACCGTTGCACGTACCGATGATGAAGCGACGACCAGCGTCGAGATTACCGGTAAGGGTTCTGACAAAGTGGTTGACGGTAGCAAAGTGACCTTCGTGGTCACCTGGAGCACCGATTTCAGCAAAGATCTGGCGGACATTATTAAAGCGGACGATCTGAAGATCAGCGCGGCCAAGGGCAACGACGTGAGCACGGTGAAAACGCAGATTGAAACCGTGCTGACCGCGGCAGGCCTGGTTAACGGTACCGACTATGTCGACTTCACGGTTGCTCGCACGGACGACGAAGCCACCACCAGCGTGGAGATCACGGGTAAAGGCAGCGATAAGGTTGTGGACGGTAGCAAAGTGACGTTCGTGGTTACCTGGAGCACCGATTTCAGCAAAGACCTGGCCGACATCATCAAGGCAGACGACCTGAAGATCAGCGCAGCTAAGGGCAATGACGACAGCGCTGTTAAGACGCAGATTGAGACCGTGCTGACCGCAGCAGGCCTGGTCAACGGTACGGATTACGTCGACTTTACGGTTGCGCGCACGGACGATGAGGCGACCACCAGCGTTGAAATCACCGGTAAGGGTAGCGATAAAGTCGTCGACGGCAGCAAAGTCACCTTCGTGGTCACCTGGAGCACCGATTTCTCTAAGTATTTGGCGGATATCATCAAGGCAGACGACTTGAAGATTAGCGCGGCAAAGGGCAATGACGCAAGCGCGGTGAAAATCCAGATCGAAACGGTCCTGACCGCCGCAGGCCTGGTCAACGGTACCGACTACGTCGATTTTACCGTCGCACGCACGGACGACGAGGCAACGACCAGCGTCGAAATTACGGGTAAGGGTAGCGACAAAGTTGTGGATGGTAGCAAAGTGACCTTTGTTGTCACCTGGTCCACCGATTTCAGCAAGGATCTGGCAGACATTATTAAAGCGGATGATCTGAAAATCTCCGCCGCGAAAGGCAACGACGTTAGCACCGTTAAAACCCAGATCGAGACGGTCCTGACCGCAGCCGGCCTGGTCAATGGCACGGACTATGTGGACTTCACCGTTGCCCGTACCGACGATGAGGCCACCACCAGCGTTGAGATCACCGGCAAAGGTAGCGATAAGGTGGTTGATGGTAGCAAGGTCACGTTCGTTGTGACCTGGAGCACCGACAGCGGTAACGGTGAAGAGCCGGAGAGCGAAGCACTGAGCATCTTTAGCTATAGCATCATTAGCGATAAGTATTCTAAC"
+	codonTable := codon.ReadCodonJSON(dataDir + "freqB.json")
+	restrictionEnzymes := []string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}
+	_, _, err := FixCdsSimple(complexGene, codonTable, restrictionEnzymes)
 	if err != nil {
 		t.Errorf("Failed to fix complex gene with error: %s", err)
-		fmt.Println(sequence)
-		fmt.Println(changes)
 	}
 }