From 27152b01d936f4b1e50e965051dfb6ad149c1ebd Mon Sep 17 00:00:00 2001 From: Koeng101 Date: Mon, 27 Sep 2021 08:44:35 -0700 Subject: [PATCH] Add fragmentation to synthesis directory (#198) * Moved synthesis to fixer and wrote fragment --- {transform => synthesis}/codon/codon.go | 0 {transform => synthesis}/codon/codon_test.go | 0 synthesis/{ => fix}/example_test.go | 10 +- synthesis/{ => fix}/synthesis.go | 26 ++-- synthesis/{ => fix}/synthesis_test.go | 58 ++++----- synthesis/fragment/data.go | 9 ++ synthesis/fragment/example_test.go | 16 +++ synthesis/fragment/fragment.go | 120 +++++++++++++++++++ synthesis/fragment/fragment_test.go | 71 +++++++++++ 9 files changed, 263 insertions(+), 47 deletions(-) rename {transform => synthesis}/codon/codon.go (100%) rename {transform => synthesis}/codon/codon_test.go (100%) rename synthesis/{ => fix}/example_test.go (89%) rename synthesis/{ => fix}/synthesis.go (94%) rename synthesis/{ => fix}/synthesis_test.go (93%) create mode 100644 synthesis/fragment/data.go create mode 100644 synthesis/fragment/example_test.go create mode 100644 synthesis/fragment/fragment.go create mode 100644 synthesis/fragment/fragment_test.go diff --git a/transform/codon/codon.go b/synthesis/codon/codon.go similarity index 100% rename from transform/codon/codon.go rename to synthesis/codon/codon.go diff --git a/transform/codon/codon_test.go b/synthesis/codon/codon_test.go similarity index 100% rename from transform/codon/codon_test.go rename to synthesis/codon/codon_test.go diff --git a/synthesis/example_test.go b/synthesis/fix/example_test.go similarity index 89% rename from synthesis/example_test.go rename to synthesis/fix/example_test.go index bed3d8e4..912e54ad 100644 --- a/synthesis/example_test.go +++ b/synthesis/fix/example_test.go @@ -1,9 +1,9 @@ -package synthesis_test +package fix_test import ( "fmt" - "github.com/TimothyStiles/poly/synthesis" - "github.com/TimothyStiles/poly/transform/codon" + "github.com/TimothyStiles/poly/synthesis/codon" + "github.com/TimothyStiles/poly/synthesis/fix" ) // This example shows basic usage of the synthesis package. In this example, @@ -14,11 +14,11 @@ func Example_basic() { // Here, we initialize a codon table. This table is used to pick the // appropriate new synonymous codons. - codonTable := codon.ReadCodonJSON("../data/pichiaTable.json") + codonTable := codon.ReadCodonJSON("../../data/pichiaTable.json") // Finally, we fix the sequence with the optimization table, getting // rid of the BsaI cut site, GGTCTC - fixedSeq, _, _ := synthesis.FixCdsSimple(bla, codonTable, []string{"GGTCTC"}) + fixedSeq, _, _ := fix.CdsSimple(bla, codonTable, []string{"GGTCTC"}) fmt.Println(fixedSeq) // Output: ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA diff --git a/synthesis/synthesis.go b/synthesis/fix/synthesis.go similarity index 94% rename from synthesis/synthesis.go rename to synthesis/fix/synthesis.go index b12a16c6..ae591870 100644 --- a/synthesis/synthesis.go +++ b/synthesis/fix/synthesis.go @@ -1,5 +1,5 @@ /* -Package synthesis fixes synthetic DNA molecules in preparation for synthesis. +Package fix fixes synthetic DNA molecules in preparation for synthesis. Many synthesis companies have restrictions on the DNA they can synthesize. This synthesis fixer takes advantage of synonymous codons in protein coding @@ -11,14 +11,14 @@ This synthesis fixer is meant to cover the majority of use cases for DNA fixing. It is not intended to cover all possible use cases, since the majority of DNA design does not actually have these edge cases. -For most users, using `FixCdsSimple` will be sufficient to prepare a sequence +For most users, using `CdsSimple` will be sufficient to prepare a sequence for synthesis (you may want to add in restriction enzyme sites to remove). -FixCds does not guarantee that all requested features will be removed. If you -have use case that FixCds cannot properly fix, please put an issue in the poly +Cds does not guarantee that all requested features will be removed. If you +have use case that Cds cannot properly fix, please put an issue in the poly github. */ -package synthesis +package fix import ( "errors" @@ -29,8 +29,8 @@ import ( "sync" "github.com/TimothyStiles/poly/checks" + "github.com/TimothyStiles/poly/synthesis/codon" "github.com/TimothyStiles/poly/transform" - "github.com/TimothyStiles/poly/transform/codon" ) // DnaSuggestion is a suggestion of a fixer, generated by a @@ -45,7 +45,7 @@ type DnaSuggestion struct { } // Change is a change to a given DNA sequence. A list of changes is given as -// the output of FixCds. +// the output of Cds. type Change struct { Position int `db:"position"` Step int `db:"step"` @@ -207,10 +207,10 @@ At the end, the user should get a fixed CDS as an output, as well as a list of changes that were done to the sequence. */ -// FixCds fixes a CDS given the CDS sequence, a codon table, a list of +// Cds fixes a CDS given the CDS sequence, a codon table, a list of // functions to solve for, and a number of iterations to attempt fixing. -// Unless you are an advanced user, you should use FixCdsSimple. -func FixCds(sequence string, codontable codon.Table, problematicSequenceFuncs []func(string, chan DnaSuggestion, *sync.WaitGroup)) (string, []Change, error) { +// Unless you are an advanced user, you should use CdsSimple. +func Cds(sequence string, codontable codon.Table, problematicSequenceFuncs []func(string, chan DnaSuggestion, *sync.WaitGroup)) (string, []Change, error) { codonLength := 3 if len(sequence)%codonLength != 0 { @@ -377,10 +377,10 @@ func FixCds(sequence string, codontable codon.Table, problematicSequenceFuncs [] } } -// FixCdsSimple is FixCds with some defaults for normal usage, including +// CdsSimple is FixCds with some defaults for normal usage, including // removing of homopolymers, removing any repeat larger than 18 base pairs, and // fixing if a CDS's gc content is above 80% or below 20% -func FixCdsSimple(sequence string, codontable codon.Table, sequencesToRemove []string) (string, []Change, error) { +func CdsSimple(sequence string, codontable codon.Table, sequencesToRemove []string) (string, []Change, error) { var functions []func(string, chan DnaSuggestion, *sync.WaitGroup) // Remove homopolymers functions = append(functions, RemoveSequence([]string{"AAAAAAAA", "GGGGGGGG"}, "Homopolymers")) @@ -394,5 +394,5 @@ func FixCdsSimple(sequence string, codontable codon.Table, sequencesToRemove []s // Ensure normal GC range functions = append(functions, GcContentFixer(0.80, 0.20)) - return FixCds(sequence, codontable, functions) + return Cds(sequence, codontable, functions) } diff --git a/synthesis/synthesis_test.go b/synthesis/fix/synthesis_test.go similarity index 93% rename from synthesis/synthesis_test.go rename to synthesis/fix/synthesis_test.go index d351bedd..30e24693 100644 --- a/synthesis/synthesis_test.go +++ b/synthesis/fix/synthesis_test.go @@ -1,4 +1,4 @@ -package synthesis +package fix import ( "fmt" @@ -6,8 +6,8 @@ import ( "sync" "testing" + "github.com/TimothyStiles/poly/synthesis/codon" "github.com/TimothyStiles/poly/transform" - "github.com/TimothyStiles/poly/transform/codon" ) /****************************************************************************** @@ -16,31 +16,31 @@ Synthesis Fixer tests begin here ******************************************************************************/ -var dataDir string = "../data/" +var dataDir string = "../../data/" -func ExampleFixCds() { +func ExampleCds() { bla := "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATACGGAAATGTTGAATACTCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA" codonTable := codon.ReadCodonJSON(dataDir + "pichiaTable.json") - fixedSeq, changes, _ := FixCds(bla, codonTable, []func(string, chan DnaSuggestion, *sync.WaitGroup){RemoveRepeat(20), RemoveSequence([]string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}, "TypeIIS restriction enzyme site")}) + fixedSeq, changes, _ := Cds(bla, codonTable, []func(string, chan DnaSuggestion, *sync.WaitGroup){RemoveRepeat(20), RemoveSequence([]string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}, "TypeIIS restriction enzyme site")}) fmt.Printf("Changed position %d from %s to %s for reason: %s. Complete sequence: %s", changes[1].Position, changes[1].From, changes[1].To, changes[1].Reason, fixedSeq) // Output: Changed position 245 from GGG to GGA for reason: TypeIIS restriction enzyme site. Complete sequence: ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATATGGAAATGTTGAATACTCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA } -func ExampleFixCdsSimple() { +func ExampleCdsSimple() { bla := "ATGAAAAAAAAAAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA" codonTable := codon.ReadCodonJSON(dataDir + "pichiaTable.json") - fixedSeq, changes, _ := FixCdsSimple(bla, codonTable, []string{"GGTCTC"}) + fixedSeq, changes, _ := CdsSimple(bla, codonTable, []string{"GGTCTC"}) fmt.Printf("Changed position %d from %s to %s for reason: %s. Complete sequence: %s", changes[0].Position, changes[0].From, changes[0].To, changes[0].Reason, fixedSeq) // Output: Changed position 1 from AAA to AAG for reason: Homopolymers. Complete sequence: ATGAAGAAAAAAAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGATCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA } -func TestFixCdsWithAlteredCodonTable(t *testing.T) { +func TestCdsWithAlteredCodonTable(t *testing.T) { bla := "ATGAAAAAAAAAAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA" codonTable := codon.ReadCodonJSON(dataDir + "alteredPichiaTable.json") @@ -48,7 +48,7 @@ func TestFixCdsWithAlteredCodonTable(t *testing.T) { var functions []func(string, chan DnaSuggestion, *sync.WaitGroup) functions = append(functions, RemoveSequence([]string{"CGTGT"}, "Should change to CGA with the Altered Picha Table, because I choose this to be highest")) - fixedSeq, changes, _ := FixCds(bla, codonTable, functions) + fixedSeq, changes, _ := Cds(bla, codonTable, functions) textChange := fmt.Sprintf("Changed position %d from %s to %s for reason: %s. Complete sequence: %s", changes[0].Position, changes[0].From, changes[0].To, changes[0].Reason, fixedSeq) shouldChangeTo := "Changed position 9 from CGT to CGA for reason: Should change to CGA with the Altered Picha Table, because I choose this to be highest. Complete sequence: ATGAAAAAAAAAAGTATTCAACATTTCCGAGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTATACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA" if textChange != shouldChangeTo { @@ -56,14 +56,14 @@ func TestFixCdsWithAlteredCodonTable(t *testing.T) { } } -func BenchmarkFixCds(b *testing.B) { +func BenchmarkCds(b *testing.B) { phusion := "MGHHHHHHHHHHSSGILDVDYITEEGKPVIRLFKKENGKFKIEHDRTFRPYIYALLRDDSKIEEVKKITGERHGKIVRIVDVEKVEKKFLGKPITVWKLYLEHPQDVPTIREKVREHPAVVDIFEYDIPFAKRYLIDKGLIPMEGEEELKILAFDIETLYHEGEEFGKGPIIMISYADENEAKVITWKNIDLPYVEVVSSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLTIGRDGSEPKMQRIGDMTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLERVAKYSMEDAKATYELGKEFLPMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWENIVYLDFRALYPSIIITHNVSPDTLNLEGCKNYDIAPQVGHKFCKDIPGFIPSLLGHLLEERQKIKTKMKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYAVIDEEGKVITRGLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKGVKIKPGMVIGYIVLRGDGPISNRAILAEEYDPKKHKYDAEYYIENQVLPAVLRILEGFGYRKEDLRYQKTRQVGLTSWLNIKKSGTGGGGATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEKQKK*" codonTable := codon.ReadCodonJSON(dataDir + "pichiaTable.json") var functions []func(string, chan DnaSuggestion, *sync.WaitGroup) functions = append(functions, RemoveSequence([]string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}, "TypeIIS restriction enzyme site.")) for i := 0; i < b.N; i++ { seq, _ := codon.Optimize(phusion, codonTable) - optimizedSeq, changes, err := FixCds(seq, codonTable, functions) + optimizedSeq, changes, err := Cds(seq, codonTable, functions) if err != nil { b.Errorf("Failed to fix phusion with error: %s", err) } @@ -87,19 +87,19 @@ func TestReversion(t *testing.T) { seq := "GGACGAGACGGC" var functions []func(string, chan DnaSuggestion, *sync.WaitGroup) functions = append(functions, RemoveSequence([]string{"GGTCTC", "CGTCTC"}, "TypeIIS restriction enzyme site.")) - _, _, err := FixCds(seq, codonTable, functions) + _, _, err := Cds(seq, codonTable, functions) if err != nil { t.Errorf("Failed with error: %s", err) } } -func TestFixCds(t *testing.T) { +func TestCds(t *testing.T) { codonTable := codon.ReadCodonJSON(dataDir + "pichiaTable.json") phusion := "MGHHHHHHHHHHSSGILDVDYITEEGKPVIRLFKKENGKFKIEHDRTFRPYIYALLRDDSKIEEVKKITGERHGKIVRIVDVEKVEKKFLGKPITVWKLYLEHPQDVPTIREKVREHPAVVDIFEYDIPFAKRYLIDKGLIPMEGEEELKILAFDIETLYHEGEEFGKGPIIMISYADENEAKVITWKNIDLPYVEVVSSEREMIKRFLRIIREKDPDIIVTYNGDSFDFPYLAKRAEKLGIKLTIGRDGSEPKMQRIGDMTAVEVKGRIHFDLYHVITRTINLPTYTLEAVYEAIFGKPKEKVYADEIAKAWESGENLERVAKYSMEDAKATYELGKEFLPMEIQLSRLVGQPLWDVSRSSTGNLVEWFLLRKAYERNEVAPNKPSEEEYQRRLRESYTGGFVKEPEKGLWENIVYLDFRALYPSIIITHNVSPDTLNLEGCKNYDIAPQVGHKFCKDIPGFIPSLLGHLLEERQKIKTKMKETQDPIEKILLDYRQKAIKLLANSFYGYYGYAKARWYCKECAESVTAWGRKYIELVWKELEEKFGFKVLYIDTDGLYATIPGGESEEIKKKALEFVKYINSKLPGLLELEYEGFYKRGFFVTKKRYAVIDEEGKVITRGLEIVRRDWSEIAKETQARVLETILKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKGVKIKPGMVIGYIVLRGDGPISNRAILAEEYDPKKHKYDAEYYIENQVLPAVLRILEGFGYRKEDLRYQKTRQVGLTSWLNIKKSGTGGGGATVKFKYKGEEKEVDISKIKKVWRVGKMISFTYDEGGGKTGRGAVSEKDAPKELLQMLEKQKK*" var functions []func(string, chan DnaSuggestion, *sync.WaitGroup) functions = append(functions, RemoveSequence([]string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}, "TypeIIS restriction enzyme site.")) seq, _ := codon.Optimize(phusion, codonTable) - optimizedSeq, _, err := FixCds(seq, codonTable, functions) + optimizedSeq, _, err := Cds(seq, codonTable, functions) if err != nil { t.Errorf("Failed with error: %s", err) } @@ -114,7 +114,7 @@ func TestFixCds(t *testing.T) { } // Does this flip back in the history? - fixedSeq, _, _ := FixCdsSimple("ATGTATTGA", codonTable, []string{"TAT"}) + fixedSeq, _, _ := CdsSimple("ATGTATTGA", codonTable, []string{"TAT"}) if fixedSeq != "ATGTACTGA" { t.Errorf("Failed to fix ATGTATTGA -> ATGTACTGA") } @@ -122,7 +122,7 @@ func TestFixCds(t *testing.T) { // Repeat checking blaWithRepeat := "ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGGGTGCCTCACTGATTAAGCATTGGTAA" functions = append(functions, RemoveRepeat(20)) - blaWithoutRepeat, _, err := FixCds(blaWithRepeat, codonTable, functions) + blaWithoutRepeat, _, err := Cds(blaWithRepeat, codonTable, functions) if err != nil { t.Errorf("Failed to remove repeat with error: %s", err) } @@ -135,26 +135,26 @@ func TestFixCds(t *testing.T) { // Test low and high GC content var gcFunctions []func(string, chan DnaSuggestion, *sync.WaitGroup) gcFunctions = append(gcFunctions, GcContentFixer(0.90, 0.10)) - fixedSeq, _, err = FixCds("GGGCCC", codonTable, gcFunctions) + fixedSeq, _, err = Cds("GGGCCC", codonTable, gcFunctions) if fixedSeq != "GGGCCA" { fmt.Println(err) t.Errorf("Failed to fix GGGCCC -> GGGCCA. Got %s", fixedSeq) } - fixedSeq, _, _ = FixCds("AAATTT", codonTable, gcFunctions) + fixedSeq, _, _ = Cds("AAATTT", codonTable, gcFunctions) if fixedSeq != "AAGTTT" { fmt.Println(err) t.Errorf("Failed to fix AAATTT -> AAGTTT. Got %s", fixedSeq) } } -func TestFixCdsBadInput(t *testing.T) { +func TestCdsBadInput(t *testing.T) { // This block tests a sequence that is not divisible by 3 codonTable := codon.ReadCodonJSON(dataDir + "pichiaTable.json") var functions []func(string, chan DnaSuggestion, *sync.WaitGroup) functions = append(functions, RemoveSequence([]string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"}, "TypeIIS restriction enzyme site")) - _, _, err := FixCds("AT", codonTable, functions) + _, _, err := Cds("AT", codonTable, functions) if err == nil { - t.Errorf("FixCds should fail with sequence input that is not divisible by 3") + t.Errorf("Cds should fail with sequence input that is not divisible by 3") } // This block tests a sequence that has a bad GC bias @@ -162,13 +162,13 @@ func TestFixCdsBadInput(t *testing.T) { c <- DnaSuggestion{0, 1, "XY", 1, "this should fail"} wg.Done() } - _, _, err = FixCds("ATG", codonTable, []func(string, chan DnaSuggestion, *sync.WaitGroup){badGcBiasFunc}) + _, _, err = Cds("ATG", codonTable, []func(string, chan DnaSuggestion, *sync.WaitGroup){badGcBiasFunc}) if err == nil { t.Errorf("XY should fail as a valid GC bias") } // This block tests something with no solution space - _, _, err = FixCds("GGG", codonTable, []func(string, chan DnaSuggestion, *sync.WaitGroup){GcContentFixer(0.10, 0.05)}) + _, _, err = Cds("GGG", codonTable, []func(string, chan DnaSuggestion, *sync.WaitGroup){GcContentFixer(0.10, 0.05)}) if err == nil { t.Errorf("There should be no solution to GGG -> less than .10 gc content.") } @@ -178,7 +178,7 @@ func TestFixCdsBadInput(t *testing.T) { c <- DnaSuggestion{1000000000000000000, 10, "GC", 1, "this should fail"} wg.Done() } - _, _, err = FixCds("ATG", codonTable, []func(string, chan DnaSuggestion, *sync.WaitGroup){outOfRangePosition}) + _, _, err = Cds("ATG", codonTable, []func(string, chan DnaSuggestion, *sync.WaitGroup){outOfRangePosition}) if err == nil { t.Errorf("outOfRangePosition should fail because it is out of range of the start and end positions of the sequence.") } @@ -188,7 +188,7 @@ func TestBtgZIComplexFix(t *testing.T) { complexGene := "ATGAAGCTGATTATTGGCGCAATGCATGAAGAATTGCAGGATTCCATCGCGTTCTATAAGCTGAATAAGGTGGAAAACGAGAAGTTCACCATTTATAAGAATGAAGAGATCATGTTTTGCATTACCGGTATCGGTCTGGTGAACGCGGCGGCGCAGCTGAGCTACATTCTGTCTAAATATGATATTGACTCCATTATTAACATCGGTACCAGCGGCGGTTGCGACAAAGAGCTGAAACAAGGCGACATCCTGATCATCGACAAGATCTATAACAGCGTGGCGGACGCCACCGCATTCGGCTACGCGTACGGCCAAGTTCCGCGTATGCCGAAGTACTATGAAACCAGCAACAAAGATATTATTAAAACCATCAGCAAGGCGAAAATTAAGAATATCGCGAGCTCCGACATCTTCATCCATTCTACGGAGCAAGTGAAGAACTTCATCAATAAAATTGAGGACAAGATTAGCGTCCTGGATATGGAGTGTTTTGCGTATGCTCAGACGGCTTATTTGTTCGAAAAGGAGTTTTCTGTGATTAAAATCATTAGCGACGTCATCGGCGAAAAGAATACCAACAACGTGCAGTTCAACGACTTTATCAAGATTGCCGGTAAGGAGATTTTGGAGATTCTGAAGAAAATTCTG" codonTable := codon.ReadCodonJSON(dataDir + "freqB.json") restrictionEnzymes := []string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"} - _, _, err := FixCdsSimple(complexGene, codonTable, restrictionEnzymes) + _, _, err := CdsSimple(complexGene, codonTable, restrictionEnzymes) if err != nil { t.Errorf("Failed to fix complex gene with error: %s", err) } @@ -198,7 +198,7 @@ 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) + _, _, err := CdsSimple(complexGene, codonTable, restrictionEnzymes) if err != nil { t.Errorf("Failed to fix complex gene with error: %s", err) } @@ -211,7 +211,7 @@ func TestTooMuchRepeat(t *testing.T) { complexGene := "ATGAAGAAACTGCTGCAACTGCTGGCTGTGCTGTCCCTGACCGCGAGCGTCCTGACCGGCATCGTTTCTTATGAGAGCATGAAAAAACTGAACAAACCGCCGGCGTATAATAAAATCGATCAAAACGAAATTCAAAAGAAGCTGGAAGAGAGCATCAAAAATAAGAACCTGACCGAAGATGAAGCCATCGCCGAGCTGAATAACAGCCTGAAGAATGTGAGCGGTATTAAAACGGTGGAAGCGAAAATTCTGACGAGCTACGCGTTCGAGGAAAAAACGTTCGAGGTTAAAGTGATGCTGGAAGAGAATTACATCTGGGACGACTTGAGCTTTAACGGTGAATTCACCGTGAGCGCGAAGGTTGGTACCTACGACGTGATCAAGAAGGAGGAAATCCAGACCATGCTGAATGAAAGCATCCAAGGCAAAAACCTGACGGAGGACGAAGCTATTGCCGAGCTGAACAATAGCCTGAAAAACGTGAGCGGCATCAAAACCGTTGAAGCCAAAATCCTGACCAGCTATGCGTTCGAGGAAAAAACGTTCGAGGTTAAAGTGATGCTGGAGGAGAACTATGTTTGGGACGACCTGAGCTTTGAGGGTAAGTTCAACGTGAATATCTCCGTTTCTAAAGTCATCAAGATTGATCAGAATGTTATGGAGAAGAGCTTCAAAAGCGCCATCCTGCAGGAGTACGACGAAAGCGAAGCCAAAAAAGCGATCATTGAAACGTTCAACAAGATTATCAATCCGGATCTGACCACGGAGCCGAAAATTGAGATCAAAAAACTGGGTGAAGTTGAATGGGATAAAGAGCATGAAATCACCATTAAGGTGAGCTTGAACACCCATAATTACGAATGGAAAAGCGAGTTCGACGGTGAATTTAAAATCAAAACCGTTCTGAATAGCACGCTGATGTTCTACAAGATCGACAAAGACGAGAACATCCACAGCAAAGAATTTAAAGGCACGAGCAGCAAAGACTGGGATGAAATTGAGTTCACCGAAATCATTGAGTTCGGTTGGTACAACAATGGTCAAGTTTGCGGTATCTTTTTCGAAGAGGACAATAATGAACCGATCAATATCTTCACCCGCTTCAGCGAAGATATTGTTTATCCGAATAAACTGAACGAGAATATCAAAAGCCTGAATTACCTGTTCTATGCGAATTCCAACTCTGGTGACCATTTGTCCGATATCAAAAAATGGGACACGAGCAATGTTAACAGCATGGAGGGCACCTTTAAACTGACCACGTTCAGCAATATTGACCTGAGCGGCTGGAACGTGTCTAATGTTACCAACATGAATTGGATCTTTGCACAGAGCGATATTGTTGATTTTGGTATCTCTAAGTGGAATACGAGCTCCGTGACCGACATGAGCAACATGTTCTACGGTGCTCAAGCGTTTAATGGTGACATTAGCACCAAGGAGGTCGATCAGAATAACGAGAAATACGTCGCCTGGGATACGAGCAAAGTCACCGACATGAGCAACATGTTTAGCGGTAGCAGCGCCTTCAATGGTGACATCTCCAAGTGGAACACCAGCTCCGTCACCAATATGAGCGGCATGTTTAGCGATACCTACGCGTTTAACGGTGACATCAGCAAGTGGAACACGAGCAGCGTCACCGACATGAGCAACATGTTTAGCCGCGCGAGCGCCTTTAACGGCGATATCAGCACCAAGGAGGTTGATCAGAACAACGAAAAATATGTCGCGTGGGACACGAGCAAAGTCACCGATATGAGCAACATGTTCTATCACACGTACGCCTTTAATGGCGATATTAGCAAATGGAACACGAGCAGCGTCACGAACATGTCTAGCATGTTCTCCGACGCTAGCGCTTTTAATGGTGATATCAGCACGAAAGAGGTTGATCAGAATAATGAGAAATACGTCGCCTGGGATACCAGCAAGGTTACCGACATGAGCAACATGTTTTACCATACCTACGCGTTCAACGGCGACATCAGCAAATGGAACACCAGCAGCGTGACGGATATGAGCAACATGTTCCTGGGTGCGCAAAATTTCAACGGTGACATCTCCACCAAAGAGGTTGACCAAAACAACGAAAAATACGTTGCGTGGGATACGTCCAAAGTCACGAACATGAGCGGTATGTTCAGCGAAGCAGAGGCGTTCAATGGCGATATTTCCAAGTGGAATACGTCCAGCGTTACGGACATGAGCAGCATGTTTAGCGGTGCGCAGGCGTTCAACGGTGACATCAGCACCAAAGAGGTGGAGAAAAATAACGAGAAATATGTTGCTTGGGACACCAGCAAAGTGACGGATATGTCCAGCATGTTTAGCGAGACCTACGCCTTTAATGGTGACATCTCCAAATGGAACACGTCCTCTGTCACGAATATGAGCAATATGTTCAGCGGTGCCCAGGCCTTCAACTGTGACATCTCCACCAAAGAGGTTGAGAAAAATAATGAGAAGTACGTGGCATGGGACACCTCCAAGGTTACGGATATGAGCTCCATGTTTTTCGGCGCACAGGCCTTTAATCAGGATATCAGCAAGTGGAATATTAGCAGCGTGACGAACATGAGCTATATGTTCTATCGCGCGCAAGCTTTCAATGTGGACATCTCCAACTGGGATGTCAAAAACGTGGAGTATTTCGCAAACTTCTACCATCAAGGTGGTAATTGGGCTAAAGAACGTCAACCGAAATTTCCGGAGAACAAC" codonTable := codon.ReadCodonJSON(dataDir + "freqB.json") restrictionEnzymes := []string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC"} - _, _, err := FixCdsSimple(complexGene, codonTable, restrictionEnzymes) + _, _, err := CdsSimple(complexGene, codonTable, restrictionEnzymes) if err == nil { t.Errorf("Succeeded in fixing complexGene") } @@ -221,7 +221,7 @@ func TestBadCodonTable(t *testing.T) { bla := "ATGAAAAAAAAAAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAA" codonTable := codon.ReadCodonJSON(dataDir + "incompletePichiaTable.json") - _, _, err := FixCdsSimple(bla, codonTable, []string{"GGTCTC"}) + _, _, err := CdsSimple(bla, codonTable, []string{"GGTCTC"}) if err == nil { t.Errorf("TestBadCodonTable should fail with 'incomplete codon table'") } @@ -235,6 +235,6 @@ func TestPanicIndex(t *testing.T) { codonTable := codon.ReadCodonJSON(dataDir + "freqB.json") gene := "ATGTCCGAAAAGAATCTGGAGCACAACCACGGTATCATCAAGGGTATCGATATTGCAGCGGAGGTGCGTAAAGACTTCCTGGAGTACAGCATGAGCGTCATCGTGAGCCGCGCACTGCCGGACCTGAAAGACGGTCTGAAACCGGTTCACCGTCGTATTATCTATGCGATGAACGACCTGGGTATCACCGCGGATAAGCCGCACAAGAAGAGCGCGCGTATCGTCGGTGAAGTTATTGGCAAGTATCACCCGCATGGTGACACCGCAGTTTATGATAGCATGGTTCGTATGGCGCAAGATTTTAGCTACCGCTATCCGCTGGTTGACGGCCACGGTAACTTTGGTAGCATCGACGGTGATGGCGCGGCGGCCATGCGTTACACCGAGGCGCGTTTGGCAAAAGTGTCCAATTTTATTATCAAGGACATCGATATGAATACCGTGCCGTTCGTGGACAACTACGACGCAAGCGAGCGTGAACCGGCTTACCTGACGGGCTATTTCCCGAATCTGCTGGCAAATGGTGCAATGGGTATCGCGGTCGGTATGGCTACCAGCATCCCGCCGCATAATCTGCGTGAGGTGATCTCCGCGATTCATGCATTTATCGATAACAAAGATATCACCATCGATGAGATCCTGGACAATCATATTATGGGTCCGGATTTCCCGACCGGTGCTCTGATGACCAACGGTATTCGTATGCGTGAGGGTTACAAAACGGGTCGCGGTGCGGTGACCATCCGCGCTAAAGTCGCACTGGAAGAGAATGATCGCCATGCGCGCTTCATCATTACGGAGATTCCGTATCAGACCAACAAGGCGAAACTGATTGAGCGCATCGCAGAGCTGGTCAAGACGAAGCAGCTGGAAGGTATCAGCGACATTCGTGACGAGAGCAATTATGAAGGTATTCGCATCGTTATCGAGCTGCGTCGCGACAGCAATCCGGACGTGGTCCTGAGCAAGCTGTACAAATTTACCAACTTGCAAACCACGTATAGCTTGAACCTGCTGAGCCTGCACAATAATATTCCGGTTCTGCTGGACCTGAAAAGCATCATCAAACACTACGTCGACTTTCAGATCAACGTTATTATCAAGCGCAGCATTTTTGAGAAGGATAAGATCGAAAAACGCTTCCACATCCTGGAAGCGCTGGATACCGCGCTGGACAATATCGACGCGATTGTCAACATTCTGCGTAACAGCCCGGAGAGCAACGAGGCTAAAATGAAGCTGACCGAAGCGTTCGGCTTCGATGAAGAACAAAATAAAGCGATCCTGGATATGCGTCTGCAACGTTTGGTCGGTCTGGAACGTGGCAAAATCCAGCAGGAGATGGCGCAGATCAAAGAGCGTATTGACTACCTGACCCTGCTGATTAGCGATGAAACCGAACAGAACAATGTTCTGAAGAACCAGCTGAGCGAAATTGCTGAGAAATTCGGTGACAACCGTCGCACGGAGACGATTGACGAGGGTCTGATGGATATCGAGGATGAGGAACTGATTCCGGACGTGAAGACGATGATTCTGCTGAGCGACGAAGGCTATATTCGTCGTGTGGATCCGGAGGAATTTCGCGTCCAAAAGCGCGGTGGTCGCGGTGTGAGCGTGAACTCCAGCAATGAGGACCCGATTGTTATCGCGACGATGGGTAAGATGCGTGACTGGGTCCTGTTTTTCACGAATAGCGGTAAGGTCTTCCGCACCAAAGCCTACAACATTCGCCAATACAGCCGTACCGCGCGCGGCCTGCCGATCGTGAATTTTCTGAACGGTCTGACCGCGGGCGACAAGATTACCGCGATTCTGCCGCTGCGTAATGTGAAAGAGAAAATGAATTATTTGACCTTTATTACCGAGAAGGGTATGATTAAGAAAACCGATATTAGCCTGTTTGACAATATCAACAAAAACGGTAAAATCGCGATTAACTTGAAAGAGGACGACCAACTGGTGACCGTTTTCGCGACCACGGGCGAGGATACCATCTTTGTGGCAAACAAGAGCGGTAAAGTTATCCGTATTCAGGAAAACATCGTCCGCCCGTTGTCTCGTACGGCATCTGGTGTGAAAGCGATTAAGTTGGACGAGAACGATGTGGTGGTGGGTGCAGTTACGAGCTTCGGTATTGAGAACATTACGACCATTTCCTCCAAGGGTAGCTTCAAAAAGACGAACATCGATGAGTATCGTATCAGCGGCCGTAATGGTAAAGGCATCAAAGTCATGAATCTGAACGAAAAGACCGGTGATTTCAAAAGCATCATTGCGGCACGCGAAACCGATCTGGTTTGTATTATTAGCACGGACGGCAATCTGATTAAGACCAAAGCGAGCGATATCCCGGTGCTGGGCCGTGCGGCTGCCGGCGTGCGTGGTATTCGCCTGTCCGAGGGTAATAAGATTCAGGCCGTTATGCTGGAGTACCGTAAACACGGTGAAGAGAACCAGGAATTCGAGGAAGAC" - _, _, _ = FixCdsSimple(gene, codonTable, []string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC", "CGTCTC"}) + _, _, _ = CdsSimple(gene, codonTable, []string{"GAAGAC", "GGTCTC", "GCGATG", "CGTCTC", "GCTCTTC", "CACCTGC", "CGTCTC"}) } diff --git a/synthesis/fragment/data.go b/synthesis/fragment/data.go new file mode 100644 index 00000000..ddd5ea84 --- /dev/null +++ b/synthesis/fragment/data.go @@ -0,0 +1,9 @@ +package fragment + +type key struct { + X, Y string +} + +var mismatches = map[key]int{ + {"AAAA", "AAAA"}: 635, {"AAAA", "AAAT"}: 8, {"AAAA", "AAAG"}: 1, {"AAAA", "AAAC"}: 3, {"AAAA", "AATA"}: 2, {"AAAA", "AATG"}: 0, {"AAAA", "AATC"}: 0, {"AAAA", "AAGA"}: 0, {"AAAA", "AAGT"}: 0, {"AAAA", "AAGG"}: 0, {"AAAA", "AAGC"}: 0, {"AAAA", "AACA"}: 0, {"AAAA", "AACT"}: 0, {"AAAA", "AACG"}: 0, {"AAAA", "AACC"}: 0, {"AAAA", "ATAA"}: 7, {"AAAA", "ATAG"}: 0, {"AAAA", "ATAC"}: 0, {"AAAA", "ATTA"}: 0, {"AAAA", "ATTG"}: 0, {"AAAA", "ATTC"}: 0, {"AAAA", "ATGA"}: 0, {"AAAA", "ATGT"}: 0, {"AAAA", "ATGG"}: 0, {"AAAA", "ATGC"}: 0, {"AAAA", "ATCA"}: 0, {"AAAA", "ATCT"}: 0, {"AAAA", "ATCG"}: 0, {"AAAA", "ATCC"}: 0, {"AAAA", "AGAA"}: 0, {"AAAA", "AGAG"}: 0, {"AAAA", "AGAC"}: 0, {"AAAA", "AGTA"}: 0, {"AAAA", "AGTG"}: 0, {"AAAA", "AGTC"}: 0, {"AAAA", "AGGA"}: 0, {"AAAA", "AGGT"}: 0, {"AAAA", "AGGG"}: 0, {"AAAA", "AGGC"}: 0, {"AAAA", "AGCA"}: 0, {"AAAA", "AGCG"}: 0, {"AAAA", "AGCC"}: 0, {"AAAA", "ACAA"}: 0, {"AAAA", "ACAG"}: 0, {"AAAA", "ACAC"}: 0, {"AAAA", "ACTA"}: 0, {"AAAA", "ACTG"}: 0, {"AAAA", "ACTC"}: 0, {"AAAA", "ACGA"}: 0, {"AAAA", "ACGG"}: 0, {"AAAA", "ACGC"}: 0, {"AAAA", "ACCA"}: 0, {"AAAA", "ACCG"}: 0, {"AAAA", "ACCC"}: 0, {"AAAA", "TAAA"}: 4, {"AAAA", "TAAG"}: 0, {"AAAA", "TAAC"}: 0, {"AAAA", "TATG"}: 0, {"AAAA", "TATC"}: 0, {"AAAA", "TAGA"}: 0, {"AAAA", "TAGG"}: 0, {"AAAA", "TAGC"}: 0, {"AAAA", "TACA"}: 0, {"AAAA", "TACG"}: 0, {"AAAA", "TACC"}: 0, {"AAAA", "TTAG"}: 0, {"AAAA", "TTAC"}: 0, {"AAAA", "TTTG"}: 1, {"AAAA", "TTTC"}: 3, {"AAAA", "TTGA"}: 0, {"AAAA", 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"TCCG"}: 82, {"CGGG", "TCCC"}: 0, {"CGGG", "GAAG"}: 0, {"CGGG", "GAAC"}: 0, {"CGGG", "GATG"}: 0, {"CGGG", "GAGG"}: 0, {"CGGG", "GAGC"}: 0, {"CGGG", "GACG"}: 0, {"CGGG", "GACC"}: 0, {"CGGG", "GTAG"}: 0, {"CGGG", "GTTG"}: 0, {"CGGG", "GTGG"}: 1, {"CGGG", "GTGC"}: 0, {"CGGG", "GTCG"}: 0, {"CGGG", "GTCC"}: 0, {"CGGG", "GGAG"}: 0, {"CGGG", "GGTG"}: 0, {"CGGG", "GGGG"}: 25, {"CGGG", "GGGC"}: 0, {"CGGG", "GGCG"}: 0, {"CGGG", "GCAG"}: 0, {"CGGG", "GCTG"}: 0, {"CGGG", "GCGG"}: 0, {"CGGG", "GCCG"}: 14, {"CGGG", "CAAG"}: 0, {"CGGG", "CAGG"}: 47, {"CGGG", "CACG"}: 50, {"CGGG", "CTGG"}: 30, {"CGGG", "CTCG"}: 20, {"CGGG", "CGGG"}: 386, +} diff --git a/synthesis/fragment/example_test.go b/synthesis/fragment/example_test.go new file mode 100644 index 00000000..0d1ea359 --- /dev/null +++ b/synthesis/fragment/example_test.go @@ -0,0 +1,16 @@ +package fragment_test + +import ( + "fmt" + "github.com/TimothyStiles/poly/synthesis/fragment" +) + +// This example shows how to use the fragmenter to fragment a gene in +// preparation for synthesis. +func Example_basic() { + lacZ := "ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG" + fragments, _, _ := fragment.Fragment(lacZ, 95, 105) + + fmt.Println(fragments) + // Output: [ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGG CTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACA AACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCG TGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG] +} diff --git a/synthesis/fragment/fragment.go b/synthesis/fragment/fragment.go new file mode 100644 index 00000000..b8ca21e5 --- /dev/null +++ b/synthesis/fragment/fragment.go @@ -0,0 +1,120 @@ +/* +Package fragment optimally fragments DNA for GoldenGate systems. + +Optimal fragmentation is accomplished by using empirical fidelity data derived +by NEB in the paper "Enabling one-pot Golden Gate assemblies of unprecedented +complexity using data-optimized assembly design". We use the BsaI-T4 ligase +data provided in table S1. + +Paper link: https://doi.org/10.1371/journal.pone.0238592 +Data link: https://doi.org/10.1371/journal.pone.0238592.s001 +*/ +package fragment + +import ( + "fmt" + "github.com/TimothyStiles/poly/transform" + "strings" +) + +// SetEfficiency gets the estimated fidelity rate of a given set of +// GoldenGate overhangs. +func SetEfficiency(overhangs []string) float64 { + var efficiency = float64(1.0) + for _, overhang := range overhangs { + nCorrect := mismatches[key{overhang, overhang}] + nTotal := 0 + for _, overhang2 := range overhangs { + nTotal = nTotal + mismatches[key{overhang, overhang2}] + } + if nTotal > 0 { + efficiency = efficiency * (float64(nCorrect) / float64(nTotal)) + } + } + return efficiency +} + +// optimizeOverhangIteration takes in a sequence and optimally fragments it. +func optimizeOverhangIteration(sequence string, minFragmentSize int, maxFragmentSize int, existingFragments []string, existingOverhangs []string) ([]string, float64, error) { + // If the sequence is smaller than maxFragment size, stop iteration. + if len(sequence) < maxFragmentSize { + existingFragments = append(existingFragments, sequence) + return existingFragments, SetEfficiency(existingOverhangs), nil + } + + // Make sure minFragmentSize > maxFragmentSize + if minFragmentSize > maxFragmentSize { + return []string{}, float64(0), fmt.Errorf("minFragmentSize (%d) larger than maxFragmentSize (%d)", minFragmentSize, maxFragmentSize) + } + + // Minimum lengths (given oligos) for assembly is 8 base pairs + // https://doi.org/10.1186/1756-0500-3-291 + // For GoldenGate, 2 8bp oligos create 12 base pairs (4bp overhangs on two sides of 4bp), + // so we check for minimal size of 12 base pairs. + if minFragmentSize < 12 { + return []string{}, float64(0), fmt.Errorf("minFragmentSize must be equal to or greater than 12 . Got size of %d", minFragmentSize) + } + + // If our iteration is approaching the end of the sequence, that means we need to gracefully handle + // the end so we aren't left with a tiny fragment that cannot be synthesized. For example, if our goal + // is fragments of 100bp, and we have 110 base pairs left, we want each final fragment to be 55bp, not + // 100 and 10bp + if len(sequence) < 2*maxFragmentSize { + maxAndMinDifference := maxFragmentSize - minFragmentSize + maxFragmentSizeBuffer := (len(sequence) + maxAndMinDifference) / 2 + if maxFragmentSizeBuffer > maxFragmentSize { + maxFragmentSizeBuffer = maxFragmentSize + } + minFragmentSize = maxFragmentSizeBuffer - maxAndMinDifference + // Basic check for minimal size + if minFragmentSize < 12 { + minFragmentSize = 12 + } + maxFragmentSize = maxFragmentSizeBuffer // buffer is needed equations above pass. + } + + // Get all sets of 4 between the min and max FragmentSize + var bestOverhangEfficiency float64 + var bestOverhangPosition int + var alreadyExists bool + for overhangOffset := 0; overhangOffset <= maxFragmentSize-minFragmentSize; overhangOffset++ { + // We go from max -> min, so we can maximize the size of our fragments + overhangPosition := maxFragmentSize - overhangOffset + overhangToTest := sequence[overhangPosition-4 : overhangPosition] + + // Make sure overhang isn't already in set + alreadyExists = false + for _, existingOverhang := range existingOverhangs { + if existingOverhang == overhangToTest || transform.ReverseComplement(existingOverhang) == overhangToTest { + alreadyExists = true + } + } + if !alreadyExists { + // Get this overhang set's efficiency + setEfficiency := SetEfficiency(append(existingOverhangs, overhangToTest)) + + // If this overhang is more efficient than any other found so far, set it as the best! + if setEfficiency > bestOverhangEfficiency { + bestOverhangEfficiency = setEfficiency + bestOverhangPosition = overhangPosition + } + } + } + // Set variables + if bestOverhangPosition == 0 { + return []string{}, float64(0), fmt.Errorf("bestOverhangPosition failed by equaling zero") + } + existingFragments = append(existingFragments, sequence[:bestOverhangPosition]) + existingOverhangs = append(existingOverhangs, sequence[bestOverhangPosition-4:bestOverhangPosition]) + sequence = sequence[bestOverhangPosition-4:] + return optimizeOverhangIteration(sequence, minFragmentSize, maxFragmentSize, existingFragments, existingOverhangs) +} + +// Fragment fragments a sequence into fragments between the min and max size, +// choosing fragment ends for optimal assembly efficiency. Since fragments will +// be insterted 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) { + sequence = strings.ToUpper(sequence) + return optimizeOverhangIteration(sequence, minFragmentSize, maxFragmentSize, []string{}, []string{sequence[:4], sequence[len(sequence)-4:]}) +} diff --git a/synthesis/fragment/fragment_test.go b/synthesis/fragment/fragment_test.go new file mode 100644 index 00000000..eaf51b45 --- /dev/null +++ b/synthesis/fragment/fragment_test.go @@ -0,0 +1,71 @@ +package fragment + +import ( + "fmt" + "testing" +) + +func ExampleFragment() { + lacZ := "ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG" + fragments, efficiency, _ := Fragment(lacZ, 95, 105) + + fmt.Printf("%s : %f", fragments[1], efficiency) + // Output: CTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACA : 1.000000 +} + +func TestFragment(t *testing.T) { + gene := "atgaaaaaatttaactggaagaaaatagtcgcgccaattgcaatgctaattattggcttactaggtggtttacttggtgcctttatcctactaacagcagccggggtatcttttaccaatacaacagatactggagtaaaaacggctaagaccgtctacaccaatataacagatacaactaaggctgttaagaaagtacaaaatgccgttgtttctgtcatcaattatcaagaaggttcatcttcagattctctaaatgacctttatggccgtatctttggcggaggggacagttctgattctagccaagaaaattcaaaagattcagatggtctacaggtcgctggtgaaggttctggagtcatctataaaaaagatggcaaagaagcctacatcgtaaccaataaccatgttgtcgatggggctaaaaaacttgaaatcatgctttcggatggttcgaaaattactggtgaacttgttggtaaagacacttactctgacctagcagttgtcaaagtatcttcagataaaataacaactgttgcagaatttgcagactcaaactcccttactgttggtgaaaaagcaattgctatcggtagcccacttggtaccgaatacgccaactcagtaacagaaggaatcgtttctagccttagccgtactataacgatgcaaaacgataatggtgaaactgtatcaacaaacgctatccaaacagatgcagccattaaccctggtaactctggtggtgccctagtcaatattgaaggacaagttatcggtattaattcaagtaaaatttcatcaacgtctgcagtcgctggtagtgctgttgaaggtatggggtttgccattccatcaaacgatgttgttgaaatcatcaatcaattagaaaaagatggtaaagttacacgaccagcactaggaatctcaatagcagatcttaatagcctttctagcagcgcaacttctaaattagatttaccagatgaggtcaaatccggtgttgttgtcggtagtgttcagaaaggtatgccagctgacggtaaacttcaagaatatgatgttatcactgagattgatggtaagaaaatcagctcaaaaactgatattcaaaccaatctttacagccatagtatcggagatactatcaaggtaaccttctatcgtggtaaagataagaaaactgtagatcttaaattaacaaaatctacagaagacatatctgattaa" + + _, _, err := Fragment(gene, 90, 110) + if err != nil { + t.Errorf(err.Error()) + } +} + +func TestUnfragmentable(t *testing.T) { + // One should not be able to fragment this + polyA := "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" + _, _, err := Fragment(polyA, 40, 80) + if err == nil { + t.Errorf("polyA should fail to fragment") + } +} + +func TestFragmentSizes(t *testing.T) { + // This tests if minSize > maxSize + lacZ := "ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG" + _, _, err := Fragment(lacZ, 105, 95) + if err == nil { + t.Errorf("Fragment should fail when minFragmentSize > maxFragmentSize") + } + + _, _, err = Fragment(lacZ, 7, 95) + if err == nil { + t.Errorf("Fragment should fail when minFragmentSize < 8") + } + +} + +func TestSmallFragmentSize(t *testing.T) { + // The following should succeed, but will require setting minFragmentSize = 12 + lacZ := "ATGACCATGATTACGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATGGTGCACTCTCAGTACAATCTGCTCTGATGCCGCATAG" + _, _, err := Fragment(lacZ, 12, 20) + if err != nil { + t.Errorf("Got error in small fragmentation: %s", err) + } +} + +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) + if err != nil { + t.Errorf(err.Error()) + } + for _, frag := range frags { + if len(frag) > 94 { + t.Errorf("Fragment too long. Expected <94, got %d", len(frag)) + } + } +}