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fixed bug that produced wrong overhang in linear, non-directional, si…
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…ngle cut reactions. (#408)

* fixed bug that produced wrong overhang in linear, non-directional, single cut reactions.
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TimothyStiles committed Dec 1, 2023
1 parent 916c92d commit d0f6ab3
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25 changes: 1 addition & 24 deletions CHANGELOG.md
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Expand Up @@ -7,28 +7,5 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [Unreleased]

### Added
- Alternative start codons can now be used in the `synthesis/codon` DNA -> protein translation package (#305)
- Added a parser and writer for the `pileup` sequence alignment format (#329)
- Added statistics to the `synthesis/codon` package (keeping track of the observed start codon occurrences in a translation table) (#350)
- Added option to fragmenter to fragment with only certain overhangs (#387)




### Fixed
- `fastq` parser no longer becomes de-aligned when reading (#325)
- `fastq` now handles optionals correctly (#323)
- No more data race in GoldenGate (#276)

### Breaking
- CutWithEnzymeByName is now a receiver of EnzymeManager. GoldenGate now takes an Enzyme instead of the name of an enzyme.
This is an effort to remove dependence on some package level global state and build some flexibility managing enzymes
over the lifetime of the program.
- Enzyme.OverhangLen is now named Enzyme.OverhangLength

## [0.26.0] - 2023-07-22
Oops, we weren't keeping a changelog before this tag!

[unreleased]: https://github.com/TimothyStiles/poly/compare/v0.26.0...main
[0.26.0]: https://github.com/TimothyStiles/poly/releases/tag/v0.26.0
- Fixed bug that produced wrong overhang in linear, non-directional, single cut reactions. #408
10 changes: 9 additions & 1 deletion clone/clone.go
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Expand Up @@ -188,7 +188,15 @@ func CutWithEnzyme(part Part, directional bool, enzyme Enzyme) []Fragment {
// In the case of a single cut in a linear sequence, we get two fragments with only 1 stick end
fragmentSequence1 := sequence[overhangs[0].Position+overhangs[0].Length:]
fragmentSequence2 := sequence[:overhangs[0].Position]
overhangSequence := sequence[overhangs[0].Position : overhangs[0].Position+overhangs[0].Length]

var overhangSequence string

if len(forwardOverhangs) > 0 {
overhangSequence = sequence[overhangs[0].Position : overhangs[0].Position+overhangs[0].Length]
} else {
overhangSequence = sequence[overhangs[0].Position-overhangs[0].Length : overhangs[0].Position]
}

fragments = append(fragments, Fragment{fragmentSequence1, overhangSequence, ""})
fragments = append(fragments, Fragment{fragmentSequence2, "", overhangSequence})
return fragments
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37 changes: 37 additions & 0 deletions clone/clone_test.go
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Expand Up @@ -96,6 +96,43 @@ func TestCutWithEnzyme(t *testing.T) {
}
}

func TestCutWithEnzymeRegression(t *testing.T) {
sequence := "AGCTGCTGTTTAAAGCTATTACTTTGAGACC" // this is a real sequence I came across that was causing problems

part := Part{sequence, false}

// get enzymes with enzyme manager
enzymeManager := NewEnzymeManager(GetBaseRestrictionEnzymes())
bsa1, err := enzymeManager.GetEnzymeByName("BsaI")
if err != nil {
t.Errorf("Error when getting Enzyme. Got error: %s", err)
}

// cut with BsaI
fragments := CutWithEnzyme(part, false, bsa1)

// check that the fragments are correct
if len(fragments) != 2 {
t.Errorf("Expected 2 fragments, got: %d", len(fragments))
}

if fragments[0].ForwardOverhang != "ACTT" {
t.Errorf("Expected forward overhang to be ACTT, got: %s", fragments[0].ForwardOverhang)
}

if fragments[0].ReverseOverhang != "" {
t.Errorf("Expected reverse overhang to be GAGT, got: %s", fragments[0].ReverseOverhang)
}

if fragments[1].ForwardOverhang != "" {
t.Errorf("Expected forward overhang to be empty, got: %s", fragments[1].ForwardOverhang)
}

if fragments[1].ReverseOverhang != "ACTT" {
t.Errorf("Expected reverse overhang to be GAGT, got: %s", fragments[1].ReverseOverhang)
}
}

func TestCircularLigate(t *testing.T) {
// The following tests for complementing overhangs. Specific, this line:
// newSeed := Fragment{seedFragment.Sequence + seedFragment.ReverseOverhang + ReverseComplement(newFragment.Sequence), seedFragment.ForwardOverhang, ReverseComplement(newFragment.ForwardOverhang)}
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