poly

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 Go to latest Published: Jun 9, 2021 License: MIT Imports: 19 Imported by: 0

README

(Poly)merase

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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

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

Examples

Constants

View Source 
const (
	MANNER_NONE                  = iota // 0: empty
	MANNER_H                            // 1: hairpin candidate
	MANNER_HAIRPIN                      // 2: hairpin
	MANNER_SINGLE                       // 3: single
	MANNER_HELIX                        // 4: helix
	MANNER_MULTI                        // 5: multi = ..M2. [30 restriction on the left and jump on the right]
	MANNER_MULTI_eq_MULTI_plus_U        // 6: multi = multi + U
	MANNER_P_eq_MULTI                   // 7: P = (multi)
	MANNER_M2_eq_M_plus_P               // 8: M2 = M + P
	MANNER_M_eq_M2                      // 9: M = M2
	MANNER_M_eq_M_plus_U                // 10: M = M + U
	MANNER_M_eq_P                       // 11: M = P
	/* MANNER_C_eq_U, */
	/* MANNER_C_eq_P, */
	MANNER_C_eq_C_plus_U // 12: C = C + U
	MANNER_C_eq_C_plus_P // 13: C = C + P
)

What is manner?

View Source 
const ASYMMETRY_MAX_LEN int = 28
View Source 
const DefaultBeamSize int = 100
View Source 
const EXPLICIT_MAX_LEN int = 4
View Source 
const HAIRPIN_MAX_LEN int = 30
View Source 
const MIN_CUBE_PRUNING_SIZE int = 20
View Source 
const NOTON int = 5 // NUM_OF_TYPE_OF_NUCS
View Source 
const NOTOND int = 25
View Source 
const NOTONT int = 125
View Source 
const SINGLE_MAX_LEN int = 30 // NOTE: *must* <= sizeof(char), otherwise modify State::TraceInfo accordingly
View Source 
const SINGLE_MIN_LEN int = 0
View Source 
const SYMMETRIC_MAX_LEN int = 15

Variables

View Source 
var INTERNAL_MAX_LEN int = SINGLE_MAX_LEN
View Source 
var VALUE_MIN float64 = -math.MaxFloat64

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 BeamPrune 

func BeamPrune(beamstep *map[int]*State) float64

func BuildFASTA 

func BuildFASTA(sequence Sequence) []byte

BuildFASTA builds a FASTA string from a Sequence struct.

Example 
sequence := ReadFASTA("data/base.fasta") // get example data
fasta := BuildFASTA(sequence)            // build a fasta byte array
firstLine := string(bytes.Split(fasta, []byte("\n"))[0])

fmt.Println(firstLine)

Output:
>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]

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 GET_ACGU_NUM 

func GET_ACGU_NUM(x rune) int

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 LinearFold 

func LinearFold(sequence string, beamSize int) (string, float64)

Assumes valid sequence input Output: Linearfold score, structure

Example 
result, score := LinearFold("UGAGUUCUCGAUCUCUAAAAUCG", DefaultBeamSize)

fmt.Println(fmt.Sprintf("result: %v , score: %v", result, score))

Output:
result: ....................... , score: -0.22376699999999988

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 Max 

func Max(a, b int) int

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 Min 

func Min(a, b int) int

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 Parse 

func Parse(sequence string) (string, float64)

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 SET_HELIX_STACKING 

func SET_HELIX_STACKING(x rune, y rune, z rune, w rune, val bool)

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 ScoreExternalUnpaired 

func ScoreExternalUnpaired(i, j int) float64

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 WriteFASTA 

func WriteFASTA(sequence Sequence, path string)

WriteFASTA writes a Sequence struct out to FASTA.

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

sequence := ReadFASTA("data/base.fasta") // get example data

tmpFASTAFilePath := filepath.Join(tmpDataDir, "base.fasta")
WriteFASTA(sequence, tmpFASTAFilePath) // write it out again

testSequence := ReadFASTA(tmpFASTAFilePath) // read it in again

fmt.Println(testSequence.Features[0].Description)

Output:
gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]

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 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 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 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 Pair 

type Pair struct {
	// contains filtered or unexported fields
}

type PairHeap 

type PairHeap []Pair

func (PairHeap) Len 

func (h PairHeap) Len() int

func (PairHeap) Less 

func (h PairHeap) Less(i, j int) bool

func (*PairHeap) Pop 

func (h *PairHeap) Pop() interface{}

func (*PairHeap) Push 

func (h *PairHeap) Push(x interface{})

func (PairHeap) Swap 

func (h PairHeap) Swap(i, j int)

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 ParseFASTA 

func ParseFASTA(file []byte) Sequence

ParseFASTA parses a Sequence struct from a FASTA file and adds appropriate pointers to the structs.

Example 
file, _ := ioutil.ReadFile("data/base.fasta")
sequence := ParseFASTA(file)

fmt.Println(sequence.Features[0].Description)

Output:
gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]

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 ReadFASTA 

func ReadFASTA(path string) Sequence

ReadFASTA reads a Sequence struct from a FASTA file.

Example

ExampleReadFASTA shows basic usage for ReadFASTA 

sequence := ReadFASTA("data/base.fasta")
fmt.Println(sequence.Features[0].Description)

Output:
gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]

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

type State 

type State struct {
	// contains filtered or unexported fields
}

func NewState 

func NewState() *State

func (*State) Set 

func (s *State) Set(score float64, manner int)

func (*State) Set2 

func (s *State) Set2(score float64, manner int, l1 rune, l2 int)

func (*State) Set3 

func (s *State) Set3(score float64, manner int, split int)

type Tuple 

type Tuple struct {
	// contains filtered or unexported fields
}

Source Files

View all Source files

Directories

Path Synopsis
Poly command line utility installation instructions: Mac OSX brew install timothystiles/poly/poly Linux - deb/rpm Download the .deb or .rpm from the releases page https://github.com/TimothyStiles/poly/releases and install with `dpkg -i` and `rpm -i` respectively Windows Coming soon...
 Poly command line utility installation instructions: Mac OSX brew install timothystiles/poly/poly Linux - deb/rpm Download the .deb or .rpm from the releases page https://github.com/TimothyStiles/poly/releases and install with `dpkg -i` and `rpm -i` respectively Windows Coming soon...
csv_helper
dataset
rbs_analysis

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