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Improve fragment interface (#316)
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* 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 <TimothyStiles@users.noreply.github.com>
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Koeng101 and TimothyStiles authored Jul 22, 2023
1 parent 4b25a31 commit f587e72
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Showing 3 changed files with 14 additions and 12 deletions.
10 changes: 6 additions & 4 deletions synthesis/fragment/example_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand All @@ -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
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4 changes: 2 additions & 2 deletions synthesis/fragment/fragment.go
Original file line number Diff line number Diff line change
Expand Up @@ -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...))
}
12 changes: 6 additions & 6 deletions synthesis/fragment/fragment_test.go
Original file line number Diff line number Diff line change
Expand Up @@ -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())
}
Expand All @@ -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")
}
Expand All @@ -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")
}
Expand All @@ -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)
}
Expand All @@ -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())
}
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