genomelink

package
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 Go to latest Published: Feb 27, 2018 License: MIT Imports: 13 Imported by: 0

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Constants

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Variables

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Functions

This section is empty.

Types

type Chromosome 

type Chromosome string

Chromosome represents chromosome defined in GRCh37. 

const (
	Chromosome1  Chromosome = "chr1"
	Chromosome2  Chromosome = "chr2"
	Chromosome3  Chromosome = "chr3"
	Chromosome4  Chromosome = "chr4"
	Chromosome5  Chromosome = "chr5"
	Chromosome6  Chromosome = "chr6"
	Chromosome7  Chromosome = "chr7"
	Chromosome8  Chromosome = "chr8"
	Chromosome9  Chromosome = "chr9"
	Chromosome10 Chromosome = "chr10"
	Chromosome11 Chromosome = "chr11"
	Chromosome12 Chromosome = "chr12"
	Chromosome13 Chromosome = "chr13"
	Chromosome14 Chromosome = "chr14"
	Chromosome15 Chromosome = "chr15"
	Chromosome16 Chromosome = "chr16"
	Chromosome17 Chromosome = "chr17"
	Chromosome18 Chromosome = "chr18"
	Chromosome19 Chromosome = "chr19"
	Chromosome20 Chromosome = "chr20"
	Chromosome21 Chromosome = "chr21"
	Chromosome22 Chromosome = "chr22"
	ChromosomeX  Chromosome = "chrX"
	ChromosomeY  Chromosome = "chrY"
	ChromosomeM  Chromosome = "chrM"
)

type Client 

type Client struct {
	URL        *url.URL
	HTTPClient *http.Client
	Logger     *zap.Logger
}

Client represents GENOMELINK API Client.

func DefaultClient 

func DefaultClient(ctx context.Context, token string) *Client

DefaultClient returns a client that connects to GENOME LINK API.

func NewClient 

func NewClient(urlStr string, client *http.Client, logger *zap.Logger) (*Client, error)

NewClient creates a new GENOME LINK client from given url, http client, and logger.

func (*Client) Report 

func (c *Client) Report(ctx context.Context, name PhenotypeName, population Population) (Report, error)

Report fetches report API for the given phenotype and population.

func (*Client) Sequence 

func (c *Client) Sequence(ctx context.Context, region Region) (io.ReadCloser, error)

Report fetches sequence API for the given region, returns io.ReadCloser.

type Phenotype 

type Phenotype struct {
	URLName     PhenotypeName `json:"url_name"`
	DisplayName string        `json:"display_name"`
	Category    string        `json:"category"`
}

Phenotype represents phenotype definition that includes display name and category.

type PhenotypeName 

type PhenotypeName string

PhenotypeName is URL-safe phenotype name. 

const (
	PhenotypeNameAgreeableness                             PhenotypeName = "agreeableness"
	PhenotypeNameAlcoholDrinkingBehavior                   PhenotypeName = "alcohol-drinking-behavior"
	PhenotypeNameAlphaLinolenicAcid                        PhenotypeName = "alpha-linolenic-acid"
	PhenotypeNameAnger                                     PhenotypeName = "anger"
	PhenotypeNameBeardThickness                            PhenotypeName = "beard-thickness"
	PhenotypeNameBetaCarotene                              PhenotypeName = "beta-carotene"
	PhenotypeNameBitterTaste                               PhenotypeName = "bitter-taste"
	PhenotypeNameBlackHair                                 PhenotypeName = "black-hair"
	PhenotypeNameBloodGlucose                              PhenotypeName = "blood-glucose"
	PhenotypeNameBMI                                       PhenotypeName = "bmi"
	PhenotypeNameBodyFatMass                               PhenotypeName = "body-fat-mass"
	PhenotypeNameBodyFatPercentage                         PhenotypeName = "body-fat-percentage"
	PhenotypeNameBreastSize                                PhenotypeName = "breast-size"
	PhenotypeNameCaffeineConsumption                       PhenotypeName = "caffeine-consumption"
	PhenotypeNameCaffeineMetaboliteRatio                   PhenotypeName = "caffeine-metabolite-ratio"
	PhenotypeNameCalcium                                   PhenotypeName = "calcium"
	PhenotypeNameCarbohydrateIntake                        PhenotypeName = "carbohydrate-intake"
	PhenotypeNameChildhoodIntelligence                     PhenotypeName = "childhood-intelligence"
	PhenotypeNameConscientiousness                         PhenotypeName = "conscientiousness"
	PhenotypeNameDepression                                PhenotypeName = "depression"
	PhenotypeNameEggAllergy                                PhenotypeName = "egg-allergy"
	PhenotypeNameEndurancePerformance                      PhenotypeName = "endurance-performance"
	PhenotypeNameExcessiveDaytimeSleepiness                PhenotypeName = "excessive-daytime-sleepiness"
	PhenotypeNameExtraversion                              PhenotypeName = "extraversion"
	PhenotypeNameGeneticEyeColor                           PhenotypeName = "eye-color"
	PhenotypeNameFolate                                    PhenotypeName = "folate"
	PhenotypeNameFreckles                                  PhenotypeName = "freckles"
	PhenotypeNameGambling                                  PhenotypeName = "gambling"
	PhenotypeNameHarmAvoidance                             PhenotypeName = "harm-avoidance"
	PhenotypeNameHearingFunction                           PhenotypeName = "hearing-function"
	PhenotypeNameHeight                                    PhenotypeName = "height"
	PhenotypeNameHippocampalVolume                         PhenotypeName = "hippocampal-volume"
	PhenotypeNameIntelligence                              PhenotypeName = "intelligence"
	PhenotypeNameIron                                      PhenotypeName = "iron"
	PhenotypeNameJobRelatedExhaustion                      PhenotypeName = "job-related-exhaustion"
	PhenotypeNameLeanBodyMass                              PhenotypeName = "lean-body-mass"
	PhenotypeNameLobeSize                                  PhenotypeName = "lobe-size"
	PhenotypeNameLongevity                                 PhenotypeName = "longevity"
	PhenotypeNameMagnesium                                 PhenotypeName = "magnesium"
	PhenotypeNameMalePatternBaldnessAGA                    PhenotypeName = "male-pattern-baldness-aga"
	PhenotypeNameMathematicalAbility                       PhenotypeName = "mathematical-ability"
	PhenotypeNameMilkAllergy                               PhenotypeName = "milk-allergy"
	PhenotypeNameMorningPerson                             PhenotypeName = "morning-person"
	PhenotypeNameMotionSickness                            PhenotypeName = "motion-sickness"
	PhenotypeNameNeuroticism                               PhenotypeName = "neuroticism"
	PhenotypeNameNoveltySeeking                            PhenotypeName = "novelty-seeking"
	PhenotypeNameOpenness                                  PhenotypeName = "openness"
	PhenotypeNamePeanutsAllergy                            PhenotypeName = "peanuts-allergy"
	PhenotypeNamePhosphorus                                PhenotypeName = "phosphorus"
	PhenotypeNameProteinIntake                             PhenotypeName = "protein-intake"
	PhenotypeNameReadingAndSpellingAbility                 PhenotypeName = "reading-and-spelling-ability"
	PhenotypeNameRedHair                                   PhenotypeName = "red-hair"
	PhenotypeNameRedWineLiking                             PhenotypeName = "red-wine-liking"
	PhenotypeNameResponseToVitaminESupplementation         PhenotypeName = "response-to-vitamin-e-supplementation"
	PhenotypeNameRewardDependence                          PhenotypeName = "reward-dependence"
	PhenotypeNameSkinPigmentation                          PhenotypeName = "skin-pigmentation"
	PhenotypeNameSleepDuration                             PhenotypeName = "sleep-duration"
	PhenotypeNameSmellSensitivityForMalt                   PhenotypeName = "smell-sensitivity-for-malt"
	PhenotypeNameSmokingBehavior                           PhenotypeName = "smoking-behavior"
	PhenotypeNameVisceralAndSubcutaneousAdiposeTissueRatio PhenotypeName = "visceral-and-subcutaneous-adipose-tissue-ratio"
	PhenotypeNameVitaminA                                  PhenotypeName = "vitamin-a"
	PhenotypeNameVitaminB12                                PhenotypeName = "vitamin-b12"
	PhenotypeNameVitaminD                                  PhenotypeName = "vitamin-d"
	PhenotypeNameVitaminE                                  PhenotypeName = "vitamin-e"
	PhenotypeNameWaist                                     PhenotypeName = "waist"
	PhenotypeNameWaistHipRatio                             PhenotypeName = "waist-hip-ratio"
	PhenotypeNameGeneticWeight                             PhenotypeName = "weight"
	PhenotypeNameWhiteWineLiking                           PhenotypeName = "white-wine-liking"
	PhenotypeNameWordReadingAbility                        PhenotypeName = "word-reading-ability"

	PhenotypeNameLungCancer           PhenotypeName = "lung-cancer"
	PhenotypeNameColorectalCancer     PhenotypeName = "colorectal-cancer"
	PhenotypeNameGastricCancer        PhenotypeName = "gastric-cancer"
	PhenotypeNameBreastCancer         PhenotypeName = "breast-cancer"
	PhenotypeNameLiverCancer          PhenotypeName = "liver-cancer"
	PhenotypeNamePancreaticCancer     PhenotypeName = "pancreatic-cancer"
	PhenotypeNameProstateCancer       PhenotypeName = "prostate-cancer"
	PhenotypeNameType2Diabetes        PhenotypeName = "type-2-diabetes"
	PhenotypeNameMyocardialInfarction PhenotypeName = "myocardial-infarction"
	PhenotypeNameNicotineDependence   PhenotypeName = "nicotine-dependence"
)

type Population 

type Population string

Population represents population that is defined in API. 

const (
	PopulationEuropean Population = "european"
)

type Region 

type Region struct {
	Chromosome Chromosome
	Start      int
	End        int
}

Region represent region of the chromosome.

func (*Region) String 

func (r *Region) String() string

String builds the string by prescribed format.

type Report 

type Report struct {
	Summary    Summary    `json:"summary"`
	Phenotype  Phenotype  `json:"phenotype"`
	Population Population `json:"population"`
	Scores     []Score    `json:"scores"`
}

Report represents the response of report API.

type Score 

type Score struct {
	Score int    `json:"score"`
	Text  string `json:"text"`
}

Score represents the score object in report response.

type Summary 

type Summary struct {
	Text     string   `json:"text"`
	Score    int      `json:"score"`
	Warnings []string `json:"warnings"`
}

Summary represents the summary object in report response.

Source Files

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