Improve fragment interface (#316)

* Add checks for reverse sequence

* Add reverseComplement checker

* add comments

* Updated to approx even better neb calculator

* improve fragment interface

* Improve example, showing how to use existing overhangs

---------

Co-authored-by: Tim <[email protected]>

synthesis/fragment/example_test.go

@@ -7,13 +7,15 @@ import (
 )
 
 // This example shows how to use the fragmenter to fragment a gene in
-// preparation for synthesis.
+// preparation for synthesis. Inputs are the sequence, the minimal fragment
+// length, the maximum fragment length, and a list of overhangs that will
+// also be used in the assembly reaction.
 func Example_basic() {
 	lacZ := "ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG"
-	fragments, _, _ := fragment.Fragment(lacZ, 95, 105)
+	fragments, _, _ := fragment.Fragment(lacZ, 95, 105, []string{"AAAA"})
 
 	fmt.Println(fragments)
-	// Output: [ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGG CTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACA AACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCG TGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG]
+	// Output: [ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGG CTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAAC CAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGC GTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG]
 }
 
 // This example shows how to generate a new overhang onto a list of overhangs.
@@ -29,7 +31,7 @@ func ExampleNextOverhang() {
 
 func ExampleFragment() {
 	lacZ := "ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG"
-	fragments, efficiency, _ := fragment.Fragment(lacZ, 95, 105)
+	fragments, efficiency, _ := fragment.Fragment(lacZ, 95, 105, []string{})
 
 	fmt.Printf("%s : %f", fragments[1], efficiency)
 	// Output: CTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACA : 1.000000

synthesis/fragment/fragment.go

@@ -176,7 +176,7 @@ func optimizeOverhangIteration(sequence string, minFragmentSize int, maxFragment
 // choosing fragment ends for optimal assembly efficiency. Since fragments will
 // be inserted into either a vector or primer binding sites, the first 4 and
 // last 4 base pairs are the initial overhang set.
-func Fragment(sequence string, minFragmentSize int, maxFragmentSize int) ([]string, float64, error) {
+func Fragment(sequence string, minFragmentSize int, maxFragmentSize int, existingOverhangs []string) ([]string, float64, error) {
 	sequence = strings.ToUpper(sequence)
-	return optimizeOverhangIteration(sequence, minFragmentSize, maxFragmentSize, []string{}, []string{sequence[:4], sequence[len(sequence)-4:]})
+	return optimizeOverhangIteration(sequence, minFragmentSize, maxFragmentSize, []string{}, append([]string{sequence[:4], sequence[len(sequence)-4:]}, existingOverhangs...))
 }

synthesis/fragment/fragment_test.go

@@ -7,7 +7,7 @@ import (
 func TestFragment(t *testing.T) {
 	gene := "atgaaaaaatttaactggaagaaaatagtcgcgccaattgcaatgctaattattggcttactaggtggtttacttggtgcctttatcctactaacagcagccggggtatcttttaccaatacaacagatactggagtaaaaacggctaagaccgtctacaccaatataacagatacaactaaggctgttaagaaagtacaaaatgccgttgtttctgtcatcaattatcaagaaggttcatcttcagattctctaaatgacctttatggccgtatctttggcggaggggacagttctgattctagccaagaaaattcaaaagattcagatggtctacaggtcgctggtgaaggttctggagtcatctataaaaaagatggcaaagaagcctacatcgtaaccaataaccatgttgtcgatggggctaaaaaacttgaaatcatgctttcggatggttcgaaaattactggtgaacttgttggtaaagacacttactctgacctagcagttgtcaaagtatcttcagataaaataacaactgttgcagaatttgcagactcaaactcccttactgttggtgaaaaagcaattgctatcggtagcccacttggtaccgaatacgccaactcagtaacagaaggaatcgtttctagccttagccgtactataacgatgcaaaacgataatggtgaaactgtatcaacaaacgctatccaaacagatgcagccattaaccctggtaactctggtggtgccctagtcaatattgaaggacaagttatcggtattaattcaagtaaaatttcatcaacgtctgcagtcgctggtagtgctgttgaaggtatggggtttgccattccatcaaacgatgttgttgaaatcatcaatcaattagaaaaagatggtaaagttacacgaccagcactaggaatctcaatagcagatcttaatagcctttctagcagcgcaacttctaaattagatttaccagatgaggtcaaatccggtgttgttgtcggtagtgttcagaaaggtatgccagctgacggtaaacttcaagaatatgatgttatcactgagattgatggtaagaaaatcagctcaaaaactgatattcaaaccaatctttacagccatagtatcggagatactatcaaggtaaccttctatcgtggtaaagataagaaaactgtagatcttaaattaacaaaatctacagaagacatatctgattaa"
 
-	_, _, err := Fragment(gene, 90, 110)
+	_, _, err := Fragment(gene, 90, 110, []string{})
 	if err != nil {
 		t.Errorf(err.Error())
 	}
@@ -16,7 +16,7 @@ func TestFragment(t *testing.T) {
 func TestUnfragmentable(t *testing.T) {
 	// One should not be able to fragment this
 	polyA := "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
-	_, _, err := Fragment(polyA, 40, 80)
+	_, _, err := Fragment(polyA, 40, 80, []string{})
 	if err == nil {
 		t.Errorf("polyA should fail to fragment")
 	}
@@ -25,12 +25,12 @@ func TestUnfragmentable(t *testing.T) {
 func TestFragmentSizes(t *testing.T) {
 	// This tests if minSize > maxSize
 	lacZ := "ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG"
-	_, _, err := Fragment(lacZ, 105, 95)
+	_, _, err := Fragment(lacZ, 105, 95, []string{})
 	if err == nil {
 		t.Errorf("Fragment should fail when minFragmentSize > maxFragmentSize")
 	}
 
-	_, _, err = Fragment(lacZ, 7, 95)
+	_, _, err = Fragment(lacZ, 7, 95, []string{})
 	if err == nil {
 		t.Errorf("Fragment should fail when minFragmentSize < 8")
 	}
@@ -40,7 +40,7 @@ func TestFragmentSizes(t *testing.T) {
 func TestSmallFragmentSize(t *testing.T) {
 	// The following should succeed, but will require setting minFragmentSize = 12
 	lacZ := "ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG"
-	_, _, err := Fragment(lacZ, 12, 30)
+  _, _, err := Fragment(lacZ, 12, 30, []string{})
 	if err != nil {
 		t.Errorf("Got error in small fragmentation: %s", err)
 	}
@@ -50,7 +50,7 @@ func TestLongFragment(t *testing.T) {
 	// A regression test for a bug that sometimes fragmented a sequence to
 	// be longer than its max length
 	gene := "GGAGGGTCTCAATGCTGGACGATCGCAAATTCAGCGAACAGGAGCTGGTCCGTCGCAACAAATACAAAACGCTGGTCGAGCAAAACAAAGACCCGTACAAGATTACGAACTGGAAACGCAATACCACCCTGCTGAAACTGAATGAGAAATACAAAGACTATAGCAAGGAGGACCTGTTGAACCTGAATCAAGAACTGGTCGTTGTTGCAGGTCGTATCAAACTGTATCGTGAAGCCGGTAAAAAAGCTGCCTTTGTGAACATTGATGATCAAGACTCCTCTATTCAGTTGTACGTGCGCCTGGATGAGATCGGTGATCAGAGCTTCGAGGATTTCCGCAATTTCGACCTGGGTGACATCATTGGTGTTAAAGGTATCATGATGCGCACCGACCACGGCGAGTTGAGCATCCGTTGTAAGGAAGTCGTGCTGCTGAGCAAGGCCCTGCGTCCGCTGCCGGATAAACACGCGGGCATTCAGGATATTGAGGAAAAGTACCGCCGTCGCTATGTGGACCTGATTATGAATCACGACGTGCGCAAGACGTTCCAGGCGCGTACCAAGATCATTCGTACCTTGCAAAACTTTCTGGATAATAAGGGTTACATGGAGGTCGAAACCCCGATCCTGCATAGCCTGAAGGGTGGCGCGAGCGCGAAACCGTTTATTACCCACTACAATGTGCTGAATACGGATGTGTATCTGCGTATCGCGACCGAGCTGCACCTGAAACGCCTGATTGTTGGCGGTTTCGAGGGTGTGTATGAGATCGGTCGCATCTTTCGCAATGAAGGTATGTCCACGCGTCACAATCCGGAATTCACGTCTATCGAACTGTATGTCGCCTATGAGGACATGTTCTTTTTGATGGATCTGACCGAAGAGATTTTTCGCGTTTGTAATGCCGCAGTCAACAGCTCCAGCATCATTGAGTATAACAACGTGAAAATTGACCTGAGCAAGCCGTTTAAGCGCCTGCATATGGTTGACGGTATTAAACAGGTGACCGGCGTCGACTTCTGGCAGGAGATGACGGTCCAACAGGCTCTGGAGCTGGCCAAAAAGCATAAAGTGCACGTTGAAAAACATCAAGAGTCTGTTGGTCACATTATCAATTTGTTCTATGAGGAGTTCGTGGAGTCCACGATTGTTGAGCCGACGTTCGTGTACGGTCACCCGAAGGAAATCTCTCCGCTGGCTAAGAGCAATCCGTCTGACCCGCGTTTCACGGACCGTTTCGAGCTGTTCATTCTGGGTCGTGAGTATGCGAATGCGTTTAGCGAGCTGAATGACCCGATTGACCAGTACGAACGCTTCAAGGCTCAGATTGAGGAGGAAAGCAAGGGCAACGATGAAGCCAACGACATGGACATTGATTTCATCGAGGCTCTGGAACACGCCATGCCGCCGACCGCGGGTATTGGTATCGGCATTGATCGCTTGGTTATGCTGCTGACGAATAGCGAATCCATCAAAGACGTGCTGTTGTTCCCGCAAATGAAGCCGCGCGAATGAAGAGCTTAGAGACCCGCT"
-	frags, _, err := Fragment(gene, 79, 94)
+	frags, _, err := Fragment(gene, 79, 94, []string{})
 	if err != nil {
 		t.Errorf(err.Error())
 	}