poly

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 Go to latest Published: Oct 29, 2020 License: MIT Imports: 26 Imported by: 0

README

(Poly)merase · Contributor Covenant GitHub license Tests codecov PRs Welcome

Poly is a Go library and command line utility 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) 2020 Timothy Stiles

Documentation

Index

Constants

View Source 
const FIVESPACE = "     "

FIVESPACE just represents 5 space characters. Used in GBK IO

View Source 
const TAB = "\t"

TAB just represents "\t" used in GBK IO.

View Source 
const TENSPACE = FIVESPACE + FIVESPACE

TENSPACE just represents 10 space characters. Used in GBK IO

Variables

View Source 
var ComplementBaseRuneMap = map[rune]rune{
	65:  84,
	66:  86,
	67:  71,
	68:  72,
	71:  67,
	72:  68,
	75:  77,
	77:  75,
	78:  78,
	82:  89,
	83:  83,
	84:  65,
	85:  65,
	86:  66,
	87:  87,
	89:  82,
	97:  116,
	98:  118,
	99:  103,
	100: 104,
	103: 99,
	104: 100,
	107: 109,
	109: 107,
	110: 110,
	114: 121,
	115: 115,
	116: 97,
	117: 97,
	118: 98,
	119: 119,
	121: 114,
}

ComplementBaseRuneMap provides 1:1 mapping between bases and their complements

View Source 
var DefaultCodonTablesByName = map[string]CodonTable{
	"Standard":                         generateCodonTable("FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**--*----M---------------M----------------------------"),
	"VertebrateMitochondrial":          generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG", "----------**--------------------MMMM----------**---M------------"),
	"YeastMitochondrial":               generateCodonTable("FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**----------------------MM---------------M------------"),
	"MoldMitochondrial":                generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--MM------**-------M------------MMMM---------------M------------"),
	"ProtozoanMitochondrial":           generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--MM------**-------M------------MMMM---------------M------------"),
	"CoelenterateMitochondrial":        generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--MM------**-------M------------MMMM---------------M------------"),
	"Mycoplasma":                       generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--MM------**-------M------------MMMM---------------M------------"),
	"Spiroplasma":                      generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--MM------**-------M------------MMMM---------------M------------"),
	"InvertebrateMitochondrial":        generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG", "---M------**--------------------MMMM---------------M------------"),
	"CiliateNuclear":                   generateCodonTable("FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"),
	"DasycladaceanNuclear":             generateCodonTable("FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"),
	"HexamitaNuclear":                  generateCodonTable("FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"),
	"EchinodermMitochondrial":          generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "----------**-----------------------M---------------M------------"),
	"FlatwormMitochondrial":            generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "----------**-----------------------M---------------M------------"),
	"EuplotidNuclear":                  generateCodonTable("FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**-----------------------M----------------------------"),
	"BacterialPlastid":                 generateCodonTable("FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**--*----M------------MMMM---------------M------------"),
	"ArchaelPlastid":                   generateCodonTable("FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**--*----M------------MMMM---------------M------------"),
	"PlantPlastid":                     generateCodonTable("FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**--*----M------------MMMM---------------M------------"),
	"AlternativeYeastNuclear":          generateCodonTable("FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*----M---------------M----------------------------"),
	"AscidianMitochondrial":            generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG", "---M------**----------------------MM---------------M------------"),
	"AlternativeFlatwormMitochondrial": generateCodonTable("FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "-----------*-----------------------M----------------------------"),
	"ChlorophyceanMitochondrial":       generateCodonTable("FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------*---*--------------------M----------------------------"),
	"TrematodeMitochondrial":           generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "----------**-----------------------M---------------M------------"),
	"ScenedesmusObliquusMitochondrial": generateCodonTable("FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "------*---*---*--------------------M----------------------------"),
	"ThraustochytriumMitochondrial":    generateCodonTable("FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--*-------**--*-----------------M--M---------------M------------"),
	"RhabdopleuridaeMitochondrial":     generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG", "---M------**-------M---------------M---------------M------------"),
	"CandidateDivisionSR1":             generateCodonTable("FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**-----------------------M---------------M------------"),
	"Gracilibacteria":                  generateCodonTable("FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**-----------------------M---------------M------------"),
	"PachysolenTannophilusNuclear":     generateCodonTable("FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*----M---------------M----------------------------"),
	"KaryorelictNuclear":               generateCodonTable("FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"),
	"CondylostomaNuclear":              generateCodonTable("FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*--------------------M----------------------------"),
	"MesodiniumNuclear":                generateCodonTable("FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"),
	"PeritrichNuclear":                 generateCodonTable("FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"),
	"BlastocrithidiaNuclear":           generateCodonTable("FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**-----------------------M----------------------------"),

	"CephalodiscidaeMitochondrial":     generateCodonTable("FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG", "---M-------*-------M---------------M---------------M------------")} // 33

DefaultCodonTablesByName stores all codon tables published by NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi using named indeces.

View Source 
var DefaultCodonTablesByNumber = map[int]CodonTable{
	1:  generateCodonTable("FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**--*----M---------------M----------------------------"),
	2:  generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG", "----------**--------------------MMMM----------**---M------------"),
	3:  generateCodonTable("FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**----------------------MM---------------M------------"),
	4:  generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--MM------**-------M------------MMMM---------------M------------"),
	5:  generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG", "---M------**--------------------MMMM---------------M------------"),
	6:  generateCodonTable("FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"),
	9:  generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "----------**-----------------------M---------------M------------"),
	10: generateCodonTable("FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**-----------------------M----------------------------"),
	11: generateCodonTable("FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**--*----M------------MMMM---------------M------------"),
	12: generateCodonTable("FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*----M---------------M----------------------------"),
	13: generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG", "---M------**----------------------MM---------------M------------"),
	14: generateCodonTable("FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "-----------*-----------------------M----------------------------"),
	16: generateCodonTable("FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------*---*--------------------M----------------------------"),
	21: generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "----------**-----------------------M---------------M------------"),
	22: generateCodonTable("FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "------*---*---*--------------------M----------------------------"),
	23: generateCodonTable("FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--*-------**--*-----------------M--M---------------M------------"),
	24: generateCodonTable("FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG", "---M------**-------M---------------M---------------M------------"),
	25: generateCodonTable("FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M------**-----------------------M---------------M------------"),
	26: generateCodonTable("FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*----M---------------M----------------------------"),
	27: generateCodonTable("FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"),
	28: generateCodonTable("FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**--*--------------------M----------------------------"),
	29: generateCodonTable("FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"),
	30: generateCodonTable("FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------*--------------------M----------------------------"),
	31: generateCodonTable("FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------**-----------------------M----------------------------"),
	33: generateCodonTable("FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG", "---M-------*-------M---------------M---------------M------------")}

DefaultCodonTablesByNumber stores all codon tables published by NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi using numbered indeces.

Functions

func Blake3SequenceHash 

func Blake3SequenceHash(annotatedSequence AnnotatedSequence) string

Blake3SequenceHash Blake3 function doesn't use standard golang hash interface so we couldn't use it with the generic sequence hash.

func BoothLeastRotation 

func BoothLeastRotation(sequence string) int

BoothLeastRotation gets the least rotation of a circular string. https://en.wikipedia.org/wiki/Lexicographically_minimal_string_rotation this is generally over commented but I'm keeping it this way for now. - Tim

func BuildFASTA added in v0.3.0 

func BuildFASTA(annotatedSequenceArray []AnnotatedSequence) []byte

BuildFASTA builds a FASTA string from an array of AnnotatedSequence structs.

func BuildGbk added in v0.2.0 

func BuildGbk(annotatedSequence AnnotatedSequence) []byte

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

func BuildGff 

func BuildGff(annotatedSequence AnnotatedSequence) []byte

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

func ComplementBase added in v0.3.0 

func ComplementBase(basePair rune) rune

ComplementBase accepts a base pair and returns its complement base pair

func GenericSequenceHash 

func GenericSequenceHash(annotatedSequence AnnotatedSequence, hash crypto.Hash) (string, error)

GenericSequenceHash takes an AnnotatedSequence and a hash function and hashes it. from https://stackoverflow.com/questions/32620290/how-to-dynamically-switch-between-hash-algorithms-in-golang <- this had a bug I had to fix! - Tim

func GetCodonFrequency added in v0.3.0 

func GetCodonFrequency(sequence string) map[string]int

GetCodonFrequency takes a DNA sequence and returns a hashmap of its codons and their frequencies.

func MarmurDoty added in v0.3.0 

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.]

func MeltingTemp added in v0.3.0 

func MeltingTemp(sequence string) float64

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

func Optimize added in v0.3.0 

func Optimize(aminoAcids string, codonTable CodonTable) string

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

func ReverseComplement added in v0.1.0 

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.

func SantaLucia added in v0.3.0 

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]

func Translate added in v0.3.0 

func Translate(sequence string, codonTable CodonTable) string

Translate translates a codon sequence to an amino acid sequence

func WriteFASTA added in v0.3.0 

func WriteFASTA(annotatedSequenceArray []AnnotatedSequence, path string)

WriteFASTA writes an array of AnnotatedSequence structs out to FASTA.

func WriteGbk added in v0.2.0 

func WriteGbk(annotatedSequence AnnotatedSequence, path string)

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

func WriteGff 

func WriteGff(annotatedSequence AnnotatedSequence, path string)

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

func WriteJSON 

func WriteJSON(annotatedSequence AnnotatedSequence, path string)

WriteJSON writes an AnnotatedSequence struct out to json.

Types

type AminoAcid added in v0.3.0 

type AminoAcid struct {
	Letter string
	Codons []Codon
}

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

type AnnotatedSequence 

type AnnotatedSequence struct {
	Meta     Meta      `json:"meta"`
	Features []Feature `json:"features"`
	Sequence Sequence  `json:"sequence"`
}

AnnotatedSequence holds all sequence information in a single struct.

func ParseFASTA added in v0.3.0 

func ParseFASTA(fasta string) []AnnotatedSequence

ParseFASTA parses an array of AnnotatedSequence structs from a FASTA file and adds appropriate pointers to the structs.

func ParseGbk 

func ParseGbk(gbk string) AnnotatedSequence

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

func ParseGff 

func ParseGff(gff string) AnnotatedSequence

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

func ParseJSON added in v0.1.0 

func ParseJSON(file []byte) AnnotatedSequence

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

func ReadFASTA added in v0.3.0 

func ReadFASTA(path string) []AnnotatedSequence

ReadFASTA reads an array of AnnotatedSequence structs from a FASTA file.

func ReadGbk 

func ReadGbk(path string) AnnotatedSequence

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

func ReadGff 

func ReadGff(path string) AnnotatedSequence

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

func ReadJSON 

func ReadJSON(path string) AnnotatedSequence

ReadJSON reads an AnnotatedSequence JSON file.

func (AnnotatedSequence) Blake3Hash added in v0.3.0 

func (annotatedSequence AnnotatedSequence) Blake3Hash() string

Blake3Hash is a method wrapper for hashing annotatedSequence structs with Blake3.

func (AnnotatedSequence) GetSequence added in v0.3.0 

func (annotatedSequence AnnotatedSequence) GetSequence() string

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

func (AnnotatedSequence) Hash added in v0.3.0 

func (annotatedSequence AnnotatedSequence) Hash(hash crypto.Hash) string

Hash is a method wrapper for hashing annotatedSequence structs.

type Codon added in v0.3.0 

type Codon struct {
	Triplet string
	Weight  int // needs to be set to 1 for random chooser
}

Codon holds information for a codon triplet in a struct

type CodonTable added in v0.3.0 

type CodonTable struct {
	StartCodons []string
	StopCodons  []string
	AminoAcids  []AminoAcid
}

CodonTable holds information for a codon table.

func (CodonTable) CreateWeights added in v0.3.0 

func (codonTable CodonTable) CreateWeights(sequence string) CodonTable

CreateWeights weights each codon in a codon table according to input string codon frequency this function actually mutates the CodonTable struct itself and doesn't technically need to return but is useful if you want to create a copy while mutating... Not sure if deep copy is appropriate

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"`
	ParentAnnotatedSequence *AnnotatedSequence `json:"-"`
}

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

func (Feature) GetSequence added in v0.3.0 

func (feature Feature) GetSequence() string

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

type Location added in v0.1.0 

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 AnnotatedSequence struct.

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 {
	Description  string `json:"description"`
	Hash         string `json:"hash"`
	HashFunction string `json:"hash_function"`
	Sequence     string `json:"sequence"`
}

Sequence holds raw sequence information in an AnnotatedSequence struct.

func (Sequence) GetSequence added in v0.3.0 

func (sequence Sequence) GetSequence() string

GetSequence is a method to get the full sequence of an unannotated sequence you could also just use sequence.sequence but I thought it was funny to include this.

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