From 7a733c7fc12e5ddf94345aebe63df9fbcfe63fd7 Mon Sep 17 00:00:00 2001 From: Trenton Date: Sat, 4 Nov 2023 08:24:16 -0400 Subject: [PATCH] expose some enzymes --- clone/clone.go | 9 +++++++++ clone/clone_test.go | 26 ++++++++------------------ 2 files changed, 17 insertions(+), 18 deletions(-) diff --git a/clone/clone.go b/clone/clone.go index edc4caf0..886eeff8 100644 --- a/clone/clone.go +++ b/clone/clone.go @@ -355,3 +355,12 @@ func (em *EnzymeManager) GoldenGate(sequences []Part, enzymeStr string) (openCon oc, il := CircularLigate(fragments) return oc, il, nil } + +// Eventually, we want to get the data for this map from ftp://ftp.neb.com/pub/rebase +func GetBaseRestrictionEnzymes() []Enzyme { + return []Enzyme{ + {"BsaI", regexp.MustCompile("GGTCTC"), regexp.MustCompile("GAGACC"), 1, 4, "GGTCTC"}, + {"BbsI", regexp.MustCompile("GAAGAC"), regexp.MustCompile("GTCTTC"), 2, 4, "GAAGAC"}, + {"BtgZI", regexp.MustCompile("GCGATG"), regexp.MustCompile("CATCGC"), 10, 4, "GCGATG"}, + } +} diff --git a/clone/clone_test.go b/clone/clone_test.go index ab4eccda..bac49436 100644 --- a/clone/clone_test.go +++ b/clone/clone_test.go @@ -2,26 +2,16 @@ package clone import ( "fmt" - "regexp" "testing" "github.com/TimothyStiles/poly/seqhash" ) -// Eventually, we want to get the data for this map from ftp://ftp.neb.com/pub/rebase -func getBaseRestrictionEnzymes() []Enzyme { - return []Enzyme{ - {"BsaI", regexp.MustCompile("GGTCTC"), regexp.MustCompile("GAGACC"), 1, 4, "GGTCTC"}, - {"BbsI", regexp.MustCompile("GAAGAC"), regexp.MustCompile("GTCTTC"), 2, 4, "GAAGAC"}, - {"BtgZI", regexp.MustCompile("GCGATG"), regexp.MustCompile("CATCGC"), 10, 4, "GCGATG"}, - } -} - // pOpen plasmid series (https://stanford.freegenes.org/collections/open-genes/products/open-plasmids#description). I use it for essentially all my cloning. -Keoni var popen = Part{"TAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGGCCTACTATTAGCAACAACGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACCTGCACCAGTCAGTAAAACGACGGCCAGTAGTCAAAAGCCTCCGACCGGAGGCTTTTGACTTGGTTCAGGTGGAGTGGGAGTAgtcttcGCcatcgCtACTAAAagccagataacagtatgcgtatttgcgcgctgatttttgcggtataagaatatatactgatatgtatacccgaagtatgtcaaaaagaggtatgctatgaagcagcgtattacagtgacagttgacagcgacagctatcagttgctcaaggcatatatgatgtcaatatctccggtctggtaagcacaaccatgcagaatgaagcccgtcgtctgcgtgccgaacgctggaaagcggaaaatcaggaagggatggctgaggtcgcccggtttattgaaatgaacggctcttttgctgacgagaacagggGCTGGTGAAATGCAGTTTAAGGTTTACACCTATAAAAGAGAGAGCCGTTATCGTCTGTTTGTGGATGTACAGAGTGATATTATTGACACGCCCGGGCGACGGATGGTGATCCCCCTGGCCAGTGCACGTCTGCTGTCAGATAAAGTCTCCCGTGAACTTTACCCGGTGGTGCATATCGGGGATGAAAGCTGGCGCATGATGACCACCGATATGGCCAGTGTGCCGGTCTCCGTTATCGGGGAAGAAGTGGCTGATCTCAGCCACCGCGAAAATGACATCAAAAACGCCATTAACCTGATGTTCTGGGGAATATAAATGTCAGGCTCCCTTATACACAGgcgatgttgaagaccaCGCTGAGGTGTCAATCGTCGGAGCCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCATGGTCATAGCTGTTTCCTGAGAGCTTGGCAGGTGATGACACACATTAACAAATTTCGTGAGGAGTCTCCAGAAGAATGCCATTAATTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGG", true} func TestCutWithEnzymeByName(t *testing.T) { - em := NewEnzymeManager(getBaseRestrictionEnzymes()) + em := NewEnzymeManager(GetBaseRestrictionEnzymes()) _, err := em.CutWithEnzymeByName(popen, true, "EcoFake") if err == nil { t.Errorf("CutWithEnzymeByName should have failed when looking for fake restriction enzyme EcoFake") @@ -29,7 +19,7 @@ func TestCutWithEnzymeByName(t *testing.T) { } func TestCutWithEnzyme(t *testing.T) { - em := NewEnzymeManager(getBaseRestrictionEnzymes()) + em := NewEnzymeManager(GetBaseRestrictionEnzymes()) var seq Part bsai := "GGTCTCAATGC" bsaiComplement := "ATGCAGAGACC" @@ -124,7 +114,7 @@ func TestCircularLigate(t *testing.T) { } func TestGoldenGate(t *testing.T) { - em := NewEnzymeManager(getBaseRestrictionEnzymes()) + em := NewEnzymeManager(GetBaseRestrictionEnzymes()) // Here we test if the enzyme we want to use in a GoldenGate reaction does not exist in our enzyme pool fragment1 := Part{"GAAGTGCCATTCCGCCTGACCTGAAGACCAGGAGAAACACGTGGCAAACATTCCGGTCTCAAATGGAAAAGAGCAACGAAACCAACGGCTACCTTGACAGCGCTCAAGCCGGCCCTGCAGCTGGCCCGGGCGCTCCGGGTACCGCCGCGGGTCGTGCACGTCGTTGCGCGGGCTTCCTGCGGCGCCAAGCGCTGGTGCTGCTCACGGTGTCTGGTGTTCTGGCAGGCGCCGGTTTGGGCGCGGCACTGCGTGGGCTCAGCCTGAGCCGCACCCAGGTCACCTACCTGGCCTTCCCCGGCGAGATGCTGCTCCGCATGCTGCGCATGATCATCCTGCCGCTGGTGGTCTGCAGCCTGGTGTCGGGCGCCGCCTCCCTCGATGCCAGCTGCCTCGGGCGTCTGGGCGGTATCGCTGTCGCCTACTTTGGCCTCACCACACTGAGTGCCTCGGCGCTCGCCGTGGCCTTGGCGTTCATCATCAAGCCAGGATCCGGTGCGCAGACCCTTCAGTCCAGCGACCTGGGGCTGGAGGACTCGGGGCCTCCTCCTGTCCCCAAAGAAACGGTGGACTCTTTCCTCGACCTGGCCAGAAACCTGTTTCCCTCCAATCTTGTGGTTGCAGCTTTCCGTACGTATGCAACCGATTATAAAGTCGTGACCCAGAACAGCAGCTCTGGAAATGTAACCCATGAAAAGATCCCCATAGGCACTGAGATAGAAGGGATGAACATTTTAGGATTGGTCCTGTTTGCTCTGGTGTTAGGAGTGGCCTTAAAGAAACTAGGCTCCGAAGGAGAGGACCTCATCCGTTTCTTCAATTCCCTCAACGAGGCGACGATGGTGCTGGTGTCCTGGATTATGTGGTACGCGTCTTCAGGCTAGGTGGAGGCTCAGTG", false} fragment2 := Part{"GAAGTGCCATTCCGCCTGACCTGAAGACCAGTACGTACCTGTGGGCATCATGTTCCTTGTTGGAAGCAAGATCGTGGAAATGAAAGACATCATCGTGCTGGTGACCAGCCTGGGGAAATACATCTTCGCATCTATATTGGGCCACGTCATTCATGGTGGTATCGTCCTGCCGCTGATTTATTTTGTTTTCACACGAAAAAACCCATTCAGATTCCTCCTGGGCCTCCTCGCCCCATTTGCGACAGCATTTGCTACGTGCTCCAGCTCAGCGACCCTTCCCTCTATGATGAAGTGCATTGAAGAGAACAATGGTGTGGACAAGAGGATCTCCAGGTTTATTCTCCCCATCGGGGCCACCGTGAACATGGACGGAGCAGCCATCTTCCAGTGTGTGGCCGCGGTGTTCATTGCGCAACTCAACAACGTAGAGCTCAACGCAGGACAGATTTTCACCATTCTAGTGACTGCCACAGCGTCCAGTGTTGGAGCAGCAGGCGTGCCAGCTGGAGGGGTCCTCACCATTGCCATTATCCTGGAGGCCATTGGGCTGCCTACTCATGATCTGCCTCTGATCCTGGCTGTGGACTGGATTGTGGACCGGACCACCACGGTGGTGAATGTGGAAGGGGATGCCCTGGGTGCAGGCATTCTCCACCACCTGAATCAGAAGGCAACAAAGAAAGGCGAGCAGGAACTTGCTGAGGTGAAAGTGGAAGCCATCCCCAACTGCAAGTCTGAGGAGGAAACCTCGCCCCTGGTGACACACCAGAACCCCGCTGGCCCCGTGGCCAGTGCCCCAGAACTGGAATCCAAGGAGTCGGTTCTGTGAAGAGCTTAGAGACCGACGACTGCCTAAGGACATTCGCTGCGTCTTCAGGCTAGGTGGAGGCTCAGTG", false} @@ -139,7 +129,7 @@ func TestGoldenGate(t *testing.T) { } func ExampleGoldenGate() { - em := NewEnzymeManager(getBaseRestrictionEnzymes()) + em := NewEnzymeManager(GetBaseRestrictionEnzymes()) // Fragment 1 has a palindrome at its start. This isn't very common but // can occur. These two fragments are real DNA fragments used in the // FreeGenes Project. They are used because they were on my computer @@ -154,7 +144,7 @@ func ExampleGoldenGate() { } func TestSignalKilledGoldenGate(t *testing.T) { - em := NewEnzymeManager(getBaseRestrictionEnzymes()) + em := NewEnzymeManager(GetBaseRestrictionEnzymes()) // This previously would crash from using too much RAM. frag1 := Part{"AAAGCACTCTTAGGCCTCTGGAAGACATGGAGGGTCTCAAGGTGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTGCGCGTAATCTTTTGCCCTGTAAACGAAAAAACCACCTGGGTAGTCTTCGCATTTCTTAATCGGTGCCC", false} frag2 := Part{"AAAGCACTCTTAGGCCTCTGGAAGACATTGGGGAGGTGGTTTGATCGAAGGTTAAGTCAGTTGGGGAACTGCTTAACCGTGGTAACTGGCTTTCGCAGAGCACAGCAACCAAATCTGTTAGTCTTCGCATTTCTTAATCGGTGCCC", false} @@ -181,7 +171,7 @@ func TestSignalKilledGoldenGate(t *testing.T) { } func TestPanicGoldenGate(t *testing.T) { - em := NewEnzymeManager(getBaseRestrictionEnzymes()) + em := NewEnzymeManager(GetBaseRestrictionEnzymes()) // This used to panic with the message: // panic: runtime error: slice bounds out of range [:-2] [recovered] // It was from the following sequence: GAAGACATAATGGTCTTC . There are 2 intercepting BbsI sites. @@ -199,7 +189,7 @@ func TestPanicGoldenGate(t *testing.T) { } func TestCircularCutRegression(t *testing.T) { - em := NewEnzymeManager(getBaseRestrictionEnzymes()) + em := NewEnzymeManager(GetBaseRestrictionEnzymes()) // This used to error with 0 fragments since the BsaI cut site is on the other // side of the origin from its recognition site. plasmid1 := Part{"AAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCCGAGaccaagtcgcggccgcgaggtgtcaatcgtcggagtagggataacagggtaatccgctgagcaataactagcataaccccttggggcctctaaacgggtcttgaggggttttttgcatggtcatagctgtttcctgttacgccccgccctgccactcgtcgcagtactgttgtaattcattaagcattctgccgacatggaagccatcacaaacggcatgatgaacctgaatcgccagcggcatcagcaccttgtcgccttgcgtataatatttgcccatggtgaaaacgggggcgaagaagttgtccatattggccacgtttaaatcaaaactggtgaaactcacccagggattggctgacacgaaaaacatattctcaataaaccctttagggaaataggccaggttttcaccgtaacacgccacatcttgcgaatatatgtgtagaaactgccggaaatcgtcgtggtattcactccagagggatgaaaacgtttcagtttgctcatggaaaacggtgtaacaagggtgaacactatcccatatcaccagctcaccatccttcattgccatacgaaattccggatgagcattcatcaggcgggcaagaatgtgaataaaggccggataaaacttgtgcttatttttctttacggtctttaaaaaggccgtaatatccagctgaacggtctggttataggtacattgagcaactgactgaaatgcctcaaaatgttctttacgatgccattgggatatatcaacggtggtatatccagtgatttttttctccattttagcttccttagctcctgaaaatctcgataactcaaaaaatacgcccggtagtgatcttatttcattatggtgaaagttggaacctcttacgtgccgatcatttccataggctccgcccccctgacgagcatcacaaaaatcgacgctcaagtcagaggtggcgaaacccgacaggactataaagataccaggcgtttccccctggaagctccctcgtgcgctctcctgttccgaccctgccgcttaccggatacctgtccgcctttctcccttcgggaagcgtggcgctttctcatagctcacgctgtaggtatctcagttcggtgtaggtcgttcgctccaagctgggctgtgtgcacgaaccccccgttcagcccgaccgctgcgccttatccggtaactatcgtcttgagtccaacccggtaagacacgacttatcgccactggcagcagccactggtaacaggattagcagagcgaggtatgtaggcggtgctacagagttcttgaagtggtggcctaactacggctacactagaaggacagtatttggtatctgcgctctgctgaagccagttaccttcggaaaaagagttggtagctcttgatccggcaaacaaaccaccgctggtagcggtggtttttttgtttgcaagcagcagattacgcgcagaaaaaaaggatctcaagtaaaacgacggccagtagtcaaaagcctccgaccggaggcttttgacttggttcaggtggagtggcggccgcgacttgGTCTC", true} @@ -219,7 +209,7 @@ func benchmarkGoldenGate(b *testing.B, em EnzymeManager, parts []Part) { } func BenchmarkGoldenGate3Parts(b *testing.B) { - em := NewEnzymeManager(getBaseRestrictionEnzymes()) + em := NewEnzymeManager(GetBaseRestrictionEnzymes()) fragment1 := Part{"GAAGTGCCATTCCGCCTGACCTGAAGACCAGGAGAAACACGTGGCAAACATTCCGGTCTCAAATGGAAAAGAGCAACGAAACCAACGGCTACCTTGACAGCGCTCAAGCCGGCCCTGCAGCTGGCCCGGGCGCTCCGGGTACCGCCGCGGGTCGTGCACGTCGTTGCGCGGGCTTCCTGCGGCGCCAAGCGCTGGTGCTGCTCACGGTGTCTGGTGTTCTGGCAGGCGCCGGTTTGGGCGCGGCACTGCGTGGGCTCAGCCTGAGCCGCACCCAGGTCACCTACCTGGCCTTCCCCGGCGAGATGCTGCTCCGCATGCTGCGCATGATCATCCTGCCGCTGGTGGTCTGCAGCCTGGTGTCGGGCGCCGCCTCCCTCGATGCCAGCTGCCTCGGGCGTCTGGGCGGTATCGCTGTCGCCTACTTTGGCCTCACCACACTGAGTGCCTCGGCGCTCGCCGTGGCCTTGGCGTTCATCATCAAGCCAGGATCCGGTGCGCAGACCCTTCAGTCCAGCGACCTGGGGCTGGAGGACTCGGGGCCTCCTCCTGTCCCCAAAGAAACGGTGGACTCTTTCCTCGACCTGGCCAGAAACCTGTTTCCCTCCAATCTTGTGGTTGCAGCTTTCCGTACGTATGCAACCGATTATAAAGTCGTGACCCAGAACAGCAGCTCTGGAAATGTAACCCATGAAAAGATCCCCATAGGCACTGAGATAGAAGGGATGAACATTTTAGGATTGGTCCTGTTTGCTCTGGTGTTAGGAGTGGCCTTAAAGAAACTAGGCTCCGAAGGAGAGGACCTCATCCGTTTCTTCAATTCCCTCAACGAGGCGACGATGGTGCTGGTGTCCTGGATTATGTGGTACGCGTCTTCAGGCTAGGTGGAGGCTCAGTG", false} fragment2 := Part{"GAAGTGCCATTCCGCCTGACCTGAAGACCAGTACGTACCTGTGGGCATCATGTTCCTTGTTGGAAGCAAGATCGTGGAAATGAAAGACATCATCGTGCTGGTGACCAGCCTGGGGAAATACATCTTCGCATCTATATTGGGCCACGTCATTCATGGTGGTATCGTCCTGCCGCTGATTTATTTTGTTTTCACACGAAAAAACCCATTCAGATTCCTCCTGGGCCTCCTCGCCCCATTTGCGACAGCATTTGCTACGTGCTCCAGCTCAGCGACCCTTCCCTCTATGATGAAGTGCATTGAAGAGAACAATGGTGTGGACAAGAGGATCTCCAGGTTTATTCTCCCCATCGGGGCCACCGTGAACATGGACGGAGCAGCCATCTTCCAGTGTGTGGCCGCGGTGTTCATTGCGCAACTCAACAACGTAGAGCTCAACGCAGGACAGATTTTCACCATTCTAGTGACTGCCACAGCGTCCAGTGTTGGAGCAGCAGGCGTGCCAGCTGGAGGGGTCCTCACCATTGCCATTATCCTGGAGGCCATTGGGCTGCCTACTCATGATCTGCCTCTGATCCTGGCTGTGGACTGGATTGTGGACCGGACCACCACGGTGGTGAATGTGGAAGGGGATGCCCTGGGTGCAGGCATTCTCCACCACCTGAATCAGAAGGCAACAAAGAAAGGCGAGCAGGAACTTGCTGAGGTGAAAGTGGAAGCCATCCCCAACTGCAAGTCTGAGGAGGAAACCTCGCCCCTGGTGACACACCAGAACCCCGCTGGCCCCGTGGCCAGTGCCCCAGAACTGGAATCCAAGGAGTCGGTTCTGTGAAGAGCTTAGAGACCGACGACTGCCTAAGGACATTCGCTGCGTCTTCAGGCTAGGTGGAGGCTCAGTG", false}