poly

README

(Poly)merase

Poly is a Go package for engineering organisms.

• Fast: Poly is fast and scalable.

• Modern: Poly tackles issues that other libraries and utilities just don't. From general codon optimization and primer design to circular sequence hashing. All written in a language that was designed to be fast, scalable, and easy to develop in and maintain. Did we say it was fast?

• Reproducible: Poly is well tested and designed to be used in industrial, academic, and hobbyist settings. No more copy and pasting strings into random websites to process the data you need.

• Ambitious: Poly's goal is to be the most complete, open, and well used collection of computational synthetic biology tools ever assembled. If you like our dream and want to support us please star this repo, request a feature, open a pull request, or sponsor the project.

Documentation

• Installation
• Library
• CLI
• Roadmap
• Learning Synbio

Community

• Discord: Chat about Poly and join us for game nights on our discord server!

Contributing

• Code of conduct: Please read the full text so you can understand what we're all about and remember to be excellent to each other!

• Contributor's guide: Please read through it before you start hacking away and pushing contributions to this fine codebase.

Sponsor

• Sponsor: 🤘 Thanks for your support 🤘

License

• MIT

• Copyright (c) 2021 Timothy Stiles

Documentation

Overview

Package poly is a go package for engineering organisms.

Poly can be used in two ways.

1. As a Go library where you have finer control and can make magical things happen.
2. As a command line utility where you can bash script your way to greatness and make DNA go brrrrrrrr.

Installation

These instructions assume that you already have a working go environment. If not see:

https://golang.org/doc/install

Building Poly CLI and package from scratch:

git clone https://github.com/TimothyStiles/poly.git && cd poly && go build ./... && go install ./...

Installing latest release of poly as a go package:

go get github.com/TimothyStiles/poly

For CLI only instructions please checkout: https://pkg.go.dev/github.com/TimothyStiles/poly/poly

Index

• func AllVariantsIUPAC(seq string) ([]string, error)
• func BuildGbk(sequence Sequence) []byte
• func BuildGff(sequence Sequence) []byte
• func ComplementBase(basePair rune) rune
• func CreateBarcodes(length int, maxSubSequence int) []string
• func CreateBarcodesWithBannedSequences(length int, maxSubSequence int, bannedSequences []string, ...) []string
• func Hash(sequence string, sequenceType string, circular bool, doubleStranded bool) (string, error)
• func IsPalindromic(sequence string) bool
• func MarmurDoty(sequence string) float64
• func MeltingTemp(sequence string) float64
• func NucleobaseDeBruijnSequence(substringLength int) string
• func Optimize(aminoAcids string, codonTable CodonTable) (string, error)
• func RandomProteinSequence(length int, seed int64) (string, error)
• func ReverseComplement(sequence string) string
• func RotateSequence(sequence string) string
• func SantaLucia(sequence string, ...) (meltingTemp, dH, dS float64)
• func Translate(sequence string, codonTable CodonTable) (string, error)
• func WriteCodonJSON(codontable CodonTable, path string)
• func WriteGbk(sequence Sequence, path string)
• func WriteGff(sequence Sequence, path string)
• func WriteJSON(sequence Sequence, path string)
• type AminoAcid
• type CloneSequence
  • func CircularLigate(fragments []Fragment) []CloneSequence
  • func GoldenGate(sequences []CloneSequence, enzymeStr string) ([]CloneSequence, error)
• type Codon
• type CodonTable
  • func AddCodonTable(firstCodonTable CodonTable, secondCodonTable CodonTable) CodonTable
  • func CompromiseCodonTable(firstCodonTable CodonTable, secondCodonTable CodonTable, cutOff float64) (CodonTable, error)
  • func GetCodonTable(index int) CodonTable
  • func ParseCodonJSON(file []byte) CodonTable
  • func ReadCodonJSON(path string) CodonTable
  • func (codonTable CodonTable) OptimizeTable(sequence string) CodonTable
• type Enzyme
• type Feature
  • func (feature Feature) GetSequence() string
• type Fragment
  • func CutWithEnzyme(seq CloneSequence, directional bool, enzyme Enzyme) []Fragment
  • func CutWithEnzymeByName(seq CloneSequence, directional bool, enzymeStr string) ([]Fragment, error)
• type Location
• type Locus
• type Meta
• type Overhang
• type Reference
• type Sequence
  • func ParseGbk(file []byte) Sequence
  • func ParseGbkFlat(file []byte) []Sequence
  • func ParseGbkMulti(file []byte) []Sequence
  • func ParseGff(file []byte) Sequence
  • func ParseJSON(file []byte) Sequence
  • func ReadGbk(path string) Sequence
  • func ReadGbkFlat(path string) []Sequence
  • func ReadGbkFlatGz(path string) []Sequence
  • func ReadGbkMulti(path string) []Sequence
  • func ReadGff(path string) Sequence
  • func ReadJSON(path string) Sequence
  • func (sequence *Sequence) AddFeature(feature Feature) []Feature
  • func (sequence Sequence) GetOptimizationTable(codonTable CodonTable) CodonTable
  • func (sequence Sequence) GetSequence() string
  • func (sequence Sequence) Hash() (string, error)

Examples

• AddCodonTable
• AllVariantsIUPAC
• BuildGbk
• BuildGff
• CompromiseCodonTable
• CreateBarcodes
• CreateBarcodesWithBannedSequences
• GoldenGate
• Hash
• MarmurDoty
• MeltingTemp
• NucleobaseDeBruijnSequence
• Optimize
• ParseCodonJSON
• ParseGbk
• ParseGbkFlat
• ParseGbkMulti
• ParseGff
• ParseJSON
• RandomProteinSequence
• ReadCodonJSON
• ReadGbk
• ReadGbkFlat
• ReadGbkFlatGz
• ReadGbkMulti
• ReadGff
• ReadJSON
• RotateSequence
• SantaLucia
• Sequence.Hash
• Translate
• WriteCodonJSON
• WriteGbk
• WriteGff
• WriteJSON

Functions

func AllVariantsIUPAC

func AllVariantsIUPAC(seq string) ([]string, error)

AllVariantsIUPAC takes a string as input and returns all iupac variants as output

Example

// AllVariantsIUPAC takes a string as input
// and returns all iupac variants as output
mendelIUPAC := "ATGGARAAYGAYGARCTN"
// ambiguous IUPAC codes for most of the sequences that code for the protein MENDEL
mendelIUPACvariants, _ := AllVariantsIUPAC(mendelIUPAC)
fmt.Println(mendelIUPACvariants)

Output:

[ATGGAGAATGATGAGCTG ATGGAGAATGATGAGCTA ATGGAGAATGATGAGCTT ATGGAGAATGATGAGCTC ATGGAGAATGATGAACTG ATGGAGAATGATGAACTA ATGGAGAATGATGAACTT ATGGAGAATGATGAACTC ATGGAGAATGACGAGCTG ATGGAGAATGACGAGCTA ATGGAGAATGACGAGCTT ATGGAGAATGACGAGCTC ATGGAGAATGACGAACTG ATGGAGAATGACGAACTA ATGGAGAATGACGAACTT ATGGAGAATGACGAACTC ATGGAGAACGATGAGCTG ATGGAGAACGATGAGCTA ATGGAGAACGATGAGCTT ATGGAGAACGATGAGCTC ATGGAGAACGATGAACTG ATGGAGAACGATGAACTA ATGGAGAACGATGAACTT ATGGAGAACGATGAACTC ATGGAGAACGACGAGCTG ATGGAGAACGACGAGCTA ATGGAGAACGACGAGCTT ATGGAGAACGACGAGCTC ATGGAGAACGACGAACTG ATGGAGAACGACGAACTA ATGGAGAACGACGAACTT ATGGAGAACGACGAACTC ATGGAAAATGATGAGCTG ATGGAAAATGATGAGCTA ATGGAAAATGATGAGCTT ATGGAAAATGATGAGCTC ATGGAAAATGATGAACTG ATGGAAAATGATGAACTA ATGGAAAATGATGAACTT ATGGAAAATGATGAACTC ATGGAAAATGACGAGCTG ATGGAAAATGACGAGCTA ATGGAAAATGACGAGCTT ATGGAAAATGACGAGCTC ATGGAAAATGACGAACTG ATGGAAAATGACGAACTA ATGGAAAATGACGAACTT ATGGAAAATGACGAACTC ATGGAAAACGATGAGCTG ATGGAAAACGATGAGCTA ATGGAAAACGATGAGCTT ATGGAAAACGATGAGCTC ATGGAAAACGATGAACTG ATGGAAAACGATGAACTA ATGGAAAACGATGAACTT ATGGAAAACGATGAACTC ATGGAAAACGACGAGCTG ATGGAAAACGACGAGCTA ATGGAAAACGACGAGCTT ATGGAAAACGACGAGCTC ATGGAAAACGACGAACTG ATGGAAAACGACGAACTA ATGGAAAACGACGAACTT ATGGAAAACGACGAACTC]

func BuildGbk

func BuildGbk(sequence Sequence) []byte

BuildGbk builds a GBK string to be written out to db or file.

Example

sequence := ReadGbk("data/puc19.gbk")
gbkBytes := BuildGbk(sequence)
testSequence := ParseGbk(gbkBytes)

fmt.Println(testSequence.Meta.Locus.ModificationDate)

Output:

22-OCT-2019

func BuildGff

func BuildGff(sequence Sequence) []byte

BuildGff takes an Annotated sequence and returns a byte array representing a gff to be written out.

Example

sequence := ReadGff("data/ecoli-mg1655-short.gff")
gffBytes := BuildGff(sequence)
reparsedSequence := ParseGff(gffBytes)

fmt.Println(reparsedSequence.Meta.Name)

Output:

U00096.3

func ComplementBase

func ComplementBase(basePair rune) rune

ComplementBase accepts a base pair and returns its complement base pair

func CreateBarcodes

func CreateBarcodes(length int, maxSubSequence int) []string

CreateBarcodes is a simplified version of CreateBarcodesWithBannedSequences with sane defaults.

Example

barcodes := CreateBarcodes(20, 4)

fmt.Println(barcodes[0])

Output:

AAAATAAAGAAACAATTAAT

func CreateBarcodesWithBannedSequences

func CreateBarcodesWithBannedSequences(length int, maxSubSequence int, bannedSequences []string, bannedFunctions []func(string) bool) []string

CreateBarcodesWithBannedSequences creates a list of barcodes given a desired barcode length, the maxSubSequence shared in each barcode, Sequences may be marked as banned by passing a static list, `bannedSequences`, or, if more flexibility is needed, through a list of `bannedFunctions` that dynamically generates bannedSequences. If a sequence is banned, it will not appear within a barcode. The a `bannedFunctions` function can determine if a barcode should be banned or not on the fly. If it is banned, we will continuing iterating until a barcode is found that satisfies the bannedFunction requirement.

Example

barcodes := CreateBarcodesWithBannedSequences(20, 4, []string{"CTCTCGGTCGCTCC"}, []func(string) bool{})

fmt.Println(barcodes[0])

Output:

AAAATAAAGAAACAATTAAT

func Hash

func Hash(sequence string, sequenceType string, circular bool, doubleStranded bool) (string, error)

Hash is a function to create Seqhashes, a specific kind of identifier.

Example

sequence := ReadGbk("data/puc19.gbk")

seqhash, _ := Hash(sequence.Sequence, "DNA", true, true)
fmt.Println(seqhash)

Output:

v1_DCD_4b0616d1b3fc632e42d78521deb38b44fba95cca9fde159e01cd567fa996ceb9

func IsPalindromic

func IsPalindromic(sequence string) bool

IsPalindromic accepts a sequence of even length and returns if it is palindromic. More here - https://en.wikipedia.org/wiki/Palindromic_sequence

func MarmurDoty

func MarmurDoty(sequence string) float64

MarmurDoty calculates the melting point of an extremely short DNA sequence (<15 bp) using a modified Marmur Doty formula [Marmur J & Doty P (1962). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol, 5, 109-118.]

Example

sequenceString := "ACGTCCGGACTT"
meltingTemp := MarmurDoty(sequenceString)

fmt.Println(meltingTemp)

Output:

31

func MeltingTemp

func MeltingTemp(sequence string) float64

MeltingTemp calls SantaLucia with default inputs for primer and salt concentration.

Example

sequenceString := "GTAAAACGACGGCCAGT" // M13 fwd
expectedTM := 52.8
meltingTemp := MeltingTemp(sequenceString)
withinMargin := math.Abs(expectedTM-meltingTemp)/expectedTM >= 0.02

fmt.Println(withinMargin)

Output:

false

func NucleobaseDeBruijnSequence

func NucleobaseDeBruijnSequence(substringLength int) string

NucleobaseDeBruijnSequence generates a DNA DeBruijn sequence with alphabet ATGC. DeBruijn sequences are basically a string with all unique substrings of an alphabet represented exactly once. Code is adapted from https://rosettacode.org/wiki/De_Bruijn_sequences#Go

Example

a := NucleobaseDeBruijnSequence(4)

fmt.Println(a)

Output:

AAAATAAAGAAACAATTAATGAATCAAGTAAGGAAGCAACTAACGAACCATATAGATACATTTATTGATTCATGTATGGATGCATCTATCGATCCAGAGACAGTTAGTGAGTCAGGTAGGGAGGCAGCTAGCGAGCCACACTTACTGACTCACGTACGGACGCACCTACCGACCCTTTTGTTTCTTGGTTGCTTCGTTCCTGTGTCTGGGTGGCTGCGTGCCTCTCGGTCGCTCCGTCCCGGGGCGGCCGCGCCCCAAA

func Optimize

func Optimize(aminoAcids string, codonTable CodonTable) (string, error)

Optimize takes an amino acid sequence and CodonTable and returns an optimized codon sequence

Example

gfpTranslation := "MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK*"

sequence := ReadGbk("data/puc19.gbk")
codonTable := GetCodonTable(11)

optimizationTable := sequence.GetOptimizationTable(codonTable)

optimizedSequence, _ := Optimize(gfpTranslation, optimizationTable)
optimizedSequenceTranslation, _ := Translate(optimizedSequence, optimizationTable)

fmt.Println(optimizedSequenceTranslation == gfpTranslation)

Output:

true

func RandomProteinSequence

func RandomProteinSequence(length int, seed int64) (string, error)

RandomProteinSequence returns a random protein sequence as a string that have size length, starts with aminoacid M (Methionine) and finishes with * (stop codon). The random generator uses the seed provided as parameter.

Example

// RandomProteinSequence builds a Protein Sequence by only passing through arguments a length and a seed that will be use to generate a randomly the sequence. The length needs to be greater than two because every sequence already have a start and stop codon. Seed makes this test deterministic.
randomProtein, _ := RandomProteinSequence(15, 2)
fmt.Println(randomProtein)

Output:

MHHPAFRMFNTMYG*

func ReverseComplement

func ReverseComplement(sequence string) string

ReverseComplement takes the reverse complement of a sequence

func RotateSequence

func RotateSequence(sequence string) string

RotateSequence rotates circular sequences to deterministic point.

Example

sequence := ReadGbk("data/puc19.gbk")
sequenceLength := len(sequence.Sequence)
testSequence := sequence.Sequence[sequenceLength/2:] + sequence.Sequence[0:sequenceLength/2]

fmt.Println(RotateSequence(sequence.Sequence) == RotateSequence(testSequence))

Output:

true

func SantaLucia

func SantaLucia(sequence string, primerConcentration, saltConcentration, magnesiumConcentration float64) (meltingTemp, dH, dS float64)

SantaLucia calculates the melting point of a short DNA sequence (15-200 bp), using the Nearest Neighbors method [SantaLucia, J. (1998) PNAS, doi:10.1073/pnas.95.4.1460]

Example

sequenceString := "ACGATGGCAGTAGCATGC" //"GTAAAACGACGGCCAGT" // M13 fwd
testCPrimer := 0.1e-6                  // primer concentration
testCNa := 350e-3                      // salt concentration
testCMg := 0.0                         // magnesium concentration
expectedTM := 62.7                     // roughly what we're expecting with a margin of error
meltingTemp, _, _ := SantaLucia(sequenceString, testCPrimer, testCNa, testCMg)
withinMargin := math.Abs(expectedTM-meltingTemp)/expectedTM >= 0.02 // checking margin of error

fmt.Println(withinMargin)

Output:

false

func Translate

func Translate(sequence string, codonTable CodonTable) (string, error)

Translate translates a codon sequence to an amino acid sequence

Example

gfpTranslation := "MASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK*"
gfpDnaSequence := "ATGGCTAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCTACATACGGAAAGCTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCTCTTATGGTGTTCAATGCTTTTCCCGTTATCCGGATCATATGAAACGGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAACGCACTATATCTTTCAAAGATGACGGGAACTACAAGACGCGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATCGTATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTCGGACACAAACTCGAGTACAACTATAACTCACACAATGTATACATCACGGCAGACAAACAAAAGAATGGAATCAAAGCTAACTTCAAAATTCGCCACAACATTGAAGATGGATCCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCGACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGCGTGACCACATGGTCCTTCTTGAGTTTGTAACTGCTGCTGGGATTACACATGGCATGGATGAGCTCTACAAATAA"
testTranslation, _ := Translate(gfpDnaSequence, GetCodonTable(11)) // need to specify which codons map to which amino acids per NCBI table

fmt.Println(gfpTranslation == testTranslation)

Output:

true

func WriteCodonJSON

func WriteCodonJSON(codontable CodonTable, path string)

WriteCodonJSON writes a CodonTable struct out to JSON.

Example

codontable := ReadCodonJSON("data/bsub_codon_test.json")
WriteCodonJSON(codontable, "data/codon_test.json")
testCodonTable := ReadCodonJSON("data/codon_test.json")

// cleaning up test data
os.Remove("data/codon_test.json")

fmt.Println(testCodonTable.AminoAcids[0].Codons[0].Weight)

Output:

28327

func WriteGbk

func WriteGbk(sequence Sequence, path string)

WriteGbk takes an Sequence struct and a path string and writes out a gff to that path.

Example

tmpDataDir, err := ioutil.TempDir("", "data-*")
if err != nil {
	fmt.Println(err.Error())
}
defer os.RemoveAll(tmpDataDir)

sequence := ReadGbk("data/puc19.gbk")

tmpGbkFilePath := filepath.Join(tmpDataDir, "puc19.gbk")
WriteGbk(sequence, tmpGbkFilePath)

testSequence := ReadGbk(tmpGbkFilePath)

fmt.Println(testSequence.Meta.Locus.ModificationDate)

Output:

22-OCT-2019

func WriteGff

func WriteGff(sequence Sequence, path string)

WriteGff takes an Sequence struct and a path string and writes out a gff to that path.

Example

tmpDataDir, err := ioutil.TempDir("", "data-*")
if err != nil {
	fmt.Println(err.Error())
}
defer os.RemoveAll(tmpDataDir)

sequence := ReadGff("data/ecoli-mg1655-short.gff")

tmpGffFilePath := filepath.Join(tmpDataDir, "ecoli-mg1655-short.gff")
WriteGff(sequence, tmpGffFilePath)

testSequence := ReadGff(tmpGffFilePath)

fmt.Println(testSequence.Meta.Name)

Output:

U00096.3

func WriteJSON

func WriteJSON(sequence Sequence, path string)

WriteJSON writes an Sequence struct out to json.

Example

tmpDataDir, err := ioutil.TempDir("", "data-*")
if err != nil {
	fmt.Println(err.Error())
}
defer os.RemoveAll(tmpDataDir)

sequence := ReadJSON("data/sample.json")

tmpJSONFilePath := filepath.Join(tmpDataDir, "sample.json")
WriteJSON(sequence, tmpJSONFilePath)

testSequence := ReadJSON(tmpJSONFilePath)

fmt.Println(testSequence.Meta.Source)

Output:

Saccharomyces cerevisiae (baker's yeast)

Types

type AminoAcid

type AminoAcid struct {
	Letter string  `json:"letter"`
	Codons []Codon `json:"codons"`
}

AminoAcid holds information for an amino acid and related codons in a struct

type CloneSequence

type CloneSequence struct {
	Sequence string
	Circular bool
}

CloneSequence is a simple struct that can carry a circular or linear DNA sequence.

func CircularLigate

func CircularLigate(fragments []Fragment) []CloneSequence

CircularLigate simulates ligation of all possible fragment combinations into circular plasmids.

func GoldenGate

func GoldenGate(sequences []CloneSequence, enzymeStr string) ([]CloneSequence, error)

GoldenGate simulates a GoldenGate cloning reaction. As of right now, we only support BsaI, BbsI, BtgZI, and BsmBI.

Example

// 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
// - Keoni
fragment1 := CloneSequence{"GAAGTGCCATTCCGCCTGACCTGAAGACCAGGAGAAACACGTGGCAAACATTCCGGTCTCAAATGGAAAAGAGCAACGAAACCAACGGCTACCTTGACAGCGCTCAAGCCGGCCCTGCAGCTGGCCCGGGCGCTCCGGGTACCGCCGCGGGTCGTGCACGTCGTTGCGCGGGCTTCCTGCGGCGCCAAGCGCTGGTGCTGCTCACGGTGTCTGGTGTTCTGGCAGGCGCCGGTTTGGGCGCGGCACTGCGTGGGCTCAGCCTGAGCCGCACCCAGGTCACCTACCTGGCCTTCCCCGGCGAGATGCTGCTCCGCATGCTGCGCATGATCATCCTGCCGCTGGTGGTCTGCAGCCTGGTGTCGGGCGCCGCCTCCCTCGATGCCAGCTGCCTCGGGCGTCTGGGCGGTATCGCTGTCGCCTACTTTGGCCTCACCACACTGAGTGCCTCGGCGCTCGCCGTGGCCTTGGCGTTCATCATCAAGCCAGGATCCGGTGCGCAGACCCTTCAGTCCAGCGACCTGGGGCTGGAGGACTCGGGGCCTCCTCCTGTCCCCAAAGAAACGGTGGACTCTTTCCTCGACCTGGCCAGAAACCTGTTTCCCTCCAATCTTGTGGTTGCAGCTTTCCGTACGTATGCAACCGATTATAAAGTCGTGACCCAGAACAGCAGCTCTGGAAATGTAACCCATGAAAAGATCCCCATAGGCACTGAGATAGAAGGGATGAACATTTTAGGATTGGTCCTGTTTGCTCTGGTGTTAGGAGTGGCCTTAAAGAAACTAGGCTCCGAAGGAGAGGACCTCATCCGTTTCTTCAATTCCCTCAACGAGGCGACGATGGTGCTGGTGTCCTGGATTATGTGGTACGCGTCTTCAGGCTAGGTGGAGGCTCAGTG", false}
fragment2 := CloneSequence{"GAAGTGCCATTCCGCCTGACCTGAAGACCAGTACGTACCTGTGGGCATCATGTTCCTTGTTGGAAGCAAGATCGTGGAAATGAAAGACATCATCGTGCTGGTGACCAGCCTGGGGAAATACATCTTCGCATCTATATTGGGCCACGTCATTCATGGTGGTATCGTCCTGCCGCTGATTTATTTTGTTTTCACACGAAAAAACCCATTCAGATTCCTCCTGGGCCTCCTCGCCCCATTTGCGACAGCATTTGCTACGTGCTCCAGCTCAGCGACCCTTCCCTCTATGATGAAGTGCATTGAAGAGAACAATGGTGTGGACAAGAGGATCTCCAGGTTTATTCTCCCCATCGGGGCCACCGTGAACATGGACGGAGCAGCCATCTTCCAGTGTGTGGCCGCGGTGTTCATTGCGCAACTCAACAACGTAGAGCTCAACGCAGGACAGATTTTCACCATTCTAGTGACTGCCACAGCGTCCAGTGTTGGAGCAGCAGGCGTGCCAGCTGGAGGGGTCCTCACCATTGCCATTATCCTGGAGGCCATTGGGCTGCCTACTCATGATCTGCCTCTGATCCTGGCTGTGGACTGGATTGTGGACCGGACCACCACGGTGGTGAATGTGGAAGGGGATGCCCTGGGTGCAGGCATTCTCCACCACCTGAATCAGAAGGCAACAAAGAAAGGCGAGCAGGAACTTGCTGAGGTGAAAGTGGAAGCCATCCCCAACTGCAAGTCTGAGGAGGAAACCTCGCCCCTGGTGACACACCAGAACCCCGCTGGCCCCGTGGCCAGTGCCCCAGAACTGGAATCCAAGGAGTCGGTTCTGTGAAGAGCTTAGAGACCGACGACTGCCTAAGGACATTCGCTGCGTCTTCAGGCTAGGTGGAGGCTCAGTG", false}

Clones, _ := GoldenGate([]CloneSequence{fragment1, fragment2, popen}, "BbsI")

fmt.Println(RotateSequence(Clones[0].Sequence))

Output:

AAAAAAAGGATCTCAAGAAGGCCTACTATTAGCAACAACGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGAACCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACCTGCACCAGTCAGTAAAACGACGGCCAGTAGTCAAAAGCCTCCGACCGGAGGCTTTTGACTTGGTTCAGGTGGAGTGGGAGAAACACGTGGCAAACATTCCGGTCTCAAATGGAAAAGAGCAACGAAACCAACGGCTACCTTGACAGCGCTCAAGCCGGCCCTGCAGCTGGCCCGGGCGCTCCGGGTACCGCCGCGGGTCGTGCACGTCGTTGCGCGGGCTTCCTGCGGCGCCAAGCGCTGGTGCTGCTCACGGTGTCTGGTGTTCTGGCAGGCGCCGGTTTGGGCGCGGCACTGCGTGGGCTCAGCCTGAGCCGCACCCAGGTCACCTACCTGGCCTTCCCCGGCGAGATGCTGCTCCGCATGCTGCGCATGATCATCCTGCCGCTGGTGGTCTGCAGCCTGGTGTCGGGCGCCGCCTCCCTCGATGCCAGCTGCCTCGGGCGTCTGGGCGGTATCGCTGTCGCCTACTTTGGCCTCACCACACTGAGTGCCTCGGCGCTCGCCGTGGCCTTGGCGTTCATCATCAAGCCAGGATCCGGTGCGCAGACCCTTCAGTCCAGCGACCTGGGGCTGGAGGACTCGGGGCCTCCTCCTGTCCCCAAAGAAACGGTGGACTCTTTCCTCGACCTGGCCAGAAACCTGTTTCCCTCCAATCTTGTGGTTGCAGCTTTCCGTACGTATGCAACCGATTATAAAGTCGTGACCCAGAACAGCAGCTCTGGAAATGTAACCCATGAAAAGATCCCCATAGGCACTGAGATAGAAGGGATGAACATTTTAGGATTGGTCCTGTTTGCTCTGGTGTTAGGAGTGGCCTTAAAGAAACTAGGCTCCGAAGGAGAGGACCTCATCCGTTTCTTCAATTCCCTCAACGAGGCGACGATGGTGCTGGTGTCCTGGATTATGTGGTACGTACCTGTGGGCATCATGTTCCTTGTTGGAAGCAAGATCGTGGAAATGAAAGACATCATCGTGCTGGTGACCAGCCTGGGGAAATACATCTTCGCATCTATATTGGGCCACGTCATTCATGGTGGTATCGTCCTGCCGCTGATTTATTTTGTTTTCACACGAAAAAACCCATTCAGATTCCTCCTGGGCCTCCTCGCCCCATTTGCGACAGCATTTGCTACGTGCTCCAGCTCAGCGACCCTTCCCTCTATGATGAAGTGCATTGAAGAGAACAATGGTGTGGACAAGAGGATCTCCAGGTTTATTCTCCCCATCGGGGCCACCGTGAACATGGACGGAGCAGCCATCTTCCAGTGTGTGGCCGCGGTGTTCATTGCGCAACTCAACAACGTAGAGCTCAACGCAGGACAGATTTTCACCATTCTAGTGACTGCCACAGCGTCCAGTGTTGGAGCAGCAGGCGTGCCAGCTGGAGGGGTCCTCACCATTGCCATTATCCTGGAGGCCATTGGGCTGCCTACTCATGATCTGCCTCTGATCCTGGCTGTGGACTGGATTGTGGACCGGACCACCACGGTGGTGAATGTGGAAGGGGATGCCCTGGGTGCAGGCATTCTCCACCACCTGAATCAGAAGGCAACAAAGAAAGGCGAGCAGGAACTTGCTGAGGTGAAAGTGGAAGCCATCCCCAACTGCAAGTCTGAGGAGGAAACCTCGCCCCTGGTGACACACCAGAACCCCGCTGGCCCCGTGGCCAGTGCCCCAGAACTGGAATCCAAGGAGTCGGTTCTGTGAAGAGCTTAGAGACCGACGACTGCCTAAGGACATTCGCTGAGGTGTCAATCGTCGGAGCCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAACGGGTCTTGAGGGGTTTTTTGCATGGTCATAGCTGTTTCCTGAGAGCTTGGCAGGTGATGACACACATTAACAAATTTCGTGAGGAGTCTCCAGAAGAATGCCATTAATTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAG

type Codon

type Codon struct {
	Triplet string `json:"triplet"`
	Weight  int    `json:"weight"` // needs to be set to 1 for random chooser
}

Codon holds information for a codon triplet in a struct

type CodonTable

type CodonTable struct {
	StartCodons []string    `json:"start_codons"`
	StopCodons  []string    `json:"stop_codons"`
	AminoAcids  []AminoAcid `json:"amino_acids"`
}

CodonTable holds information for a codon table.

func AddCodonTable

func AddCodonTable(firstCodonTable CodonTable, secondCodonTable CodonTable) CodonTable

AddCodonTable takes 2 CodonTables and adds them together to create a new CodonTable.

Example

sequence := ReadGbk("data/puc19.gbk")
codonTable := GetCodonTable(11)
optimizationTable := sequence.GetOptimizationTable(codonTable)

sequence2 := ReadGbk("data/phix174.gb")
codonTable2 := GetCodonTable(11)
optimizationTable2 := sequence2.GetOptimizationTable(codonTable2)

finalTable := AddCodonTable(optimizationTable, optimizationTable2)
for _, aa := range finalTable.AminoAcids {
	for _, codon := range aa.Codons {
		if codon.Triplet == "GGC" {
			fmt.Println(codon.Weight)
		}
	}
}

Output:

90

func CompromiseCodonTable

func CompromiseCodonTable(firstCodonTable CodonTable, secondCodonTable CodonTable, cutOff float64) (CodonTable, error)

CompromiseCodonTable takes 2 CodonTables and makes a new CodonTable that is an equal compromise between the two tables.

Example

sequence := ReadGbk("data/puc19.gbk")
codonTable := GetCodonTable(11)
optimizationTable := sequence.GetOptimizationTable(codonTable)

sequence2 := ReadGbk("data/phix174.gb")
codonTable2 := GetCodonTable(11)
optimizationTable2 := sequence2.GetOptimizationTable(codonTable2)

finalTable, _ := CompromiseCodonTable(optimizationTable, optimizationTable2, 0.1)
for _, aa := range finalTable.AminoAcids {
	for _, codon := range aa.Codons {
		if codon.Triplet == "TAA" {
			fmt.Println(codon.Weight)
		}
	}
}

Output:

2727

func GetCodonTable

func GetCodonTable(index int) CodonTable

GetCodonTable takes the index of desired NCBI codon table and returns it.

func ParseCodonJSON

func ParseCodonJSON(file []byte) CodonTable

ParseCodonJSON parses a CodonTable JSON file.

Example

file, _ := ioutil.ReadFile("data/bsub_codon_test.json")
codontable := ParseCodonJSON(file)

fmt.Println(codontable.AminoAcids[0].Codons[0].Weight)

Output:

28327

func ReadCodonJSON

func ReadCodonJSON(path string) CodonTable

ReadCodonJSON reads a CodonTable JSON file.

Example

codontable := ReadCodonJSON("data/bsub_codon_test.json")

fmt.Println(codontable.AminoAcids[0].Codons[0].Weight)

Output:

28327

func (CodonTable) OptimizeTable

func (codonTable CodonTable) OptimizeTable(sequence string) CodonTable

OptimizeTable weights each codon in a codon table according to input string codon frequency. This function actually mutates the CodonTable struct itself.

type Enzyme

type Enzyme struct {
	Name            string
	RegexpFor       *regexp.Regexp
	RegexpRev       *regexp.Regexp
	Skip            int
	OverhangLen     int
	RecognitionSite string
}

Enzyme is a struct that represents restriction enzymes.

type Feature

type Feature struct {
	Name string //Seqid in gff, name in gbk
	//gff specific
	Source               string            `json:"source"`
	Type                 string            `json:"type"`
	Score                string            `json:"score"`
	Strand               string            `json:"strand"`
	Phase                string            `json:"phase"`
	Attributes           map[string]string `json:"attributes"`
	GbkLocationString    string            `json:"gbk_location_string"`
	Sequence             string            `json:"sequence"`
	SequenceLocation     Location          `json:"sequence_location"`
	SequenceHash         string            `json:"sequence_hash"`
	Description          string            `json:"description"`
	SequenceHashFunction string            `json:"hash_function"`
	ParentSequence       *Sequence         `json:"-"`
}

Feature holds a single annotation in a struct. from https://github.com/blachlylab/gff3/blob/master/gff3.go

func (Feature) GetSequence

func (feature Feature) GetSequence() string

GetSequence is a method wrapper to get a Feature's sequence. Mutates with Sequence.

type Fragment

type Fragment struct {
	Sequence        string
	ForwardOverhang string
	ReverseOverhang string
}

Fragment is a struct that represents linear DNA sequences with sticky ends.

func CutWithEnzyme

func CutWithEnzyme(seq CloneSequence, directional bool, enzyme Enzyme) []Fragment

CutWithEnzyme cuts a given sequence with an enzyme represented by an Enzyme struct.

func CutWithEnzymeByName

func CutWithEnzymeByName(seq CloneSequence, directional bool, enzymeStr string) ([]Fragment, error)

CutWithEnzymeByName cuts a given sequence with an enzyme represented by the enzyme's name. It is a convenience wrapper around CutWithEnzyme that allows us to specify the enzyme by name.

type Location

type Location struct {
	Start             int        `json:"start"`
	End               int        `json:"end"`
	Complement        bool       `json:"complement"`
	Join              bool       `json:"join"`
	FivePrimePartial  bool       `json:"five_prime_partial"`
	ThreePrimePartial bool       `json:"three_prime_partial"`
	SubLocations      []Location `json:"sub_locations"`
}

Location holds nested location info for sequence region.

type Locus

type Locus struct {
	Name             string `json:"name"`
	SequenceLength   string `json:"sequence_length"`
	MoleculeType     string `json:"molecule_type"`
	GenbankDivision  string `json:"genbank_division"`
	ModificationDate string `json:"modification_date"`
	SequenceCoding   string `json:"sequence_coding"`
	Circular         bool   `json:"circular"`
	Linear           bool   `json:"linear"`
}

Locus holds Locus information in a Meta struct.

type Meta

type Meta struct {
	Name        string            `json:"name"`
	GffVersion  string            `json:"gff_version"`
	RegionStart int               `json:"region_start"`
	RegionEnd   int               `json:"region_end"`
	Size        int               `json:"size"`
	Type        string            `json:"type"`
	Date        string            `json:"date"`
	Definition  string            `json:"definition"`
	Accession   string            `json:"accession"`
	Version     string            `json:"version"`
	Keywords    string            `json:"keywords"`
	Organism    string            `json:"organism"`
	Source      string            `json:"source"`
	Origin      string            `json:"origin"`
	Locus       Locus             `json:"locus"`
	References  []Reference       `json:"references"`
	Other       map[string]string `json:"other"`
}

Meta Holds all the meta information of an Sequence struct.

type Overhang

type Overhang struct {
	Length   int
	Position int
	Forward  bool
}

Overhang is a struct that represents the ends of a linearized sequence where Enzymes had cut.

type Reference

type Reference struct {
	Index   string `json:"index"`
	Authors string `json:"authors"`
	Title   string `json:"title"`
	Journal string `json:"journal"`
	PubMed  string `json:"pub_med"`
	Remark  string `json:"remark"`
	Range   string `json:"range"`
}

Reference holds information one reference in a Meta struct.

type Sequence

type Sequence struct {
	Meta                 Meta      `json:"meta"`
	Description          string    `json:"description"`
	SequenceHash         string    `json:"sequence_hash"`
	SequenceHashFunction string    `json:"hash_function"`
	Sequence             string    `json:"sequence"`
	Features             []Feature `json:"features"`
}

Sequence holds all sequence information in a single struct.

func ParseGbk

func ParseGbk(file []byte) Sequence

ParseGbk takes in a string representing a gbk/gb/genbank file and parses it into an Sequence object.

Example

file, _ := ioutil.ReadFile("data/puc19.gbk")
sequence := ParseGbk(file)

fmt.Println(sequence.Meta.Locus.ModificationDate)

Output:

22-OCT-2019

func ParseGbkFlat

func ParseGbkFlat(file []byte) []Sequence

ParseGbkFlat specifically takes the output of a Genbank Flat file that from the genbank ftp dumps. These files have 10 line headers, which are entirely removed

Example

file, _ := ioutil.ReadFile("data/flatGbk_test.seq")
sequences := ParseGbkFlat(file)
var locus []string
for _, sequence := range sequences {
	locus = append(locus, sequence.Meta.Locus.Name)
}

fmt.Println(strings.Join(locus, ", "))

Output:

AB000100, AB000106

func ParseGbkMulti

func ParseGbkMulti(file []byte) []Sequence

ParseGbkMulti parses multiple Genbank files in a byte array to multiple sequences

Example

file, _ := ioutil.ReadFile("data/multiGbk_test.seq")
sequences := ParseGbkMulti(file)
var locus []string
for _, sequence := range sequences {
	locus = append(locus, sequence.Meta.Locus.Name)
}

fmt.Println(strings.Join(locus, ", "))

Output:

AB000100, AB000106

func ParseGff

func ParseGff(file []byte) Sequence

ParseGff Takes in a string representing a gffv3 file and parses it into an Sequence object.

Example

file, _ := ioutil.ReadFile("data/ecoli-mg1655-short.gff")
sequence := ParseGff(file)

fmt.Println(sequence.Meta.Name)

Output:

U00096.3

func ParseJSON

func ParseJSON(file []byte) Sequence

ParseJSON parses an Sequence JSON file and adds appropriate pointers to struct.

Example

file, _ := ioutil.ReadFile("data/sample.json")
sequence := ParseJSON(file)

fmt.Println(sequence.Meta.Source)

Output:

Saccharomyces cerevisiae (baker's yeast)

func ReadGbk

func ReadGbk(path string) Sequence

ReadGbk reads a Gbk from path and parses into an Annotated sequence struct.

Example

sequence := ReadGbk("data/puc19.gbk")
fmt.Println(sequence.Meta.Locus.ModificationDate)

Output:

22-OCT-2019

func ReadGbkFlat

func ReadGbkFlat(path string) []Sequence

ReadGbkFlat reads flat genbank files, like the ones provided by the NCBI FTP server (after decompression)

Example

sequences := ReadGbkFlat("data/long_comment.seq")
var locus []string
for _, sequence := range sequences {
	locus = append(locus, sequence.Meta.Locus.Name)
}

fmt.Println(strings.Join(locus, ", "))

Output:

AB000100, AB000106

func ReadGbkFlatGz

func ReadGbkFlatGz(path string) []Sequence

ReadGbkFlatGz reads flat gzip'd genbank files, like the ones provided by the NCBI FTP server

Example

sequences := ReadGbkFlatGz("data/flatGbk_test.seq.gz")
//sequences := ReadGbkFlatGz("data/gbbct358.seq.gz")
var locus []string
for _, sequence := range sequences {
	locus = append(locus, sequence.Meta.Locus.Name)
}
fmt.Println(strings.Join(locus, ", "))

Output:

AB000100, AB000106

func ReadGbkMulti

func ReadGbkMulti(path string) []Sequence

ReadGbkMulti reads multiple genbank files from a single file

Example

sequences := ReadGbkMulti("data/multiGbk_test.seq")
var locus []string
for _, sequence := range sequences {
	locus = append(locus, sequence.Meta.Locus.Name)
}

fmt.Println(strings.Join(locus, ", "))

Output:

AB000100, AB000106

func ReadGff

func ReadGff(path string) Sequence

ReadGff takes in a filepath for a .gffv3 file and parses it into an Annotated Sequence struct.

Example

sequence := ReadGff("data/ecoli-mg1655-short.gff")
fmt.Println(sequence.Meta.Name)

Output:

U00096.3

func ReadJSON

func ReadJSON(path string) Sequence

ReadJSON reads an Sequence JSON file.

Example

sequence := ReadJSON("data/sample.json")

fmt.Println(sequence.Meta.Source)

Output:

Saccharomyces cerevisiae (baker's yeast)

func (*Sequence) AddFeature

func (sequence *Sequence) AddFeature(feature Feature) []Feature

AddFeature is the canonical way to add a Feature into a Sequence struct. Appending a Feature struct directly to Sequence.Feature's will break .GetSequence() method.

func (Sequence) GetOptimizationTable

func (sequence Sequence) GetOptimizationTable(codonTable CodonTable) CodonTable

GetOptimizationTable is a Sequence method that takes a CodonTable and weights it to be used to optimize inserts.

func (Sequence) GetSequence

func (sequence Sequence) GetSequence() string

GetSequence is a method to get the full sequence of an annotated sequence

func (Sequence) Hash

func (sequence Sequence) Hash() (string, error)

Hash is a method wrapper for hashing Sequence structs. Note that all sequence structs are, by default, double-stranded sequences, since Genbank does not track whether or not a given sequence in their database is single stranded or double stranded.

Example

sequence := ReadGbk("data/puc19.gbk")

// Seqhash assumes doubleStranded sequence and defaults to linear
// if sequence.Meta.Locus.Circular is not set
seqhash, _ := sequence.Hash()
fmt.Println(seqhash)

Output:

v1_DCD_4b0616d1b3fc632e42d78521deb38b44fba95cca9fde159e01cd567fa996ceb9