Go API client for genome_nexus_public_api

This page shows how to use HTTP requests to access the Genome Nexus API. There are more high level clients available in Python, R, JavaScript, TypeScript and various other languages as well as a command line client to annotate MAF and VCF. See https://docs.genomenexus.org/api.

Aside from programmatic clients there are web based tools to annotate variants, see https://docs.genomenexus.org/tools.

We currently only provide long-term support for the '/annotation' endpoint. The other endpoints might change.

Overview

This API client was generated by the OpenAPI Generator project. By using the OpenAPI-spec from a remote server, you can easily generate an API client.

• API version: 2.0
• Package version: 1.0.0
• Build package: org.openapitools.codegen.languages.GoClientCodegen

Installation

Install the following dependencies:

go get github.com/stretchr/testify/assert
go get golang.org/x/oauth2
go get golang.org/x/net/context

Put the package under your project folder and add the following in import:

import genome_nexus_public_api "github.com/GIT_USER_ID/GIT_REPO_ID"

To use a proxy, set the environment variable HTTP_PROXY:

os.Setenv("HTTP_PROXY", "http://proxy_name:proxy_port")

Configuration of Server URL

Default configuration comes with Servers field that contains server objects as defined in the OpenAPI specification.

Select Server Configuration

For using other server than the one defined on index 0 set context value sw.ContextServerIndex of type int.

ctx := context.WithValue(context.Background(), genome_nexus_public_api.ContextServerIndex, 1)

Templated Server URL

Templated server URL is formatted using default variables from configuration or from context value sw.ContextServerVariables of type map[string]string.

ctx := context.WithValue(context.Background(), genome_nexus_public_api.ContextServerVariables, map[string]string{
	"basePath": "v2",
})

Note, enum values are always validated and all unused variables are silently ignored.

URLs Configuration per Operation

Each operation can use different server URL defined using OperationServers map in the Configuration. An operation is uniquely identified by "{classname}Service.{nickname}" string. Similar rules for overriding default operation server index and variables applies by using sw.ContextOperationServerIndices and sw.ContextOperationServerVariables context maps.

ctx := context.WithValue(context.Background(), genome_nexus_public_api.ContextOperationServerIndices, map[string]int{
	"{classname}Service.{nickname}": 2,
})
ctx = context.WithValue(context.Background(), genome_nexus_public_api.ContextOperationServerVariables, map[string]map[string]string{
	"{classname}Service.{nickname}": {
		"port": "8443",
	},
})

Documentation for API Endpoints

All URIs are relative to http://www.genomenexus.org

Class	Method	HTTP request	Description
AnnotationControllerApi	FetchVariantAnnotationByGenomicLocationGET	Get /annotation/genomic/{genomicLocation}	Retrieves VEP annotation for the provided genomic location
AnnotationControllerApi	FetchVariantAnnotationByGenomicLocationPOST	Post /annotation/genomic	Retrieves VEP annotation for the provided list of genomic locations
AnnotationControllerApi	FetchVariantAnnotationByIdGET	Get /annotation/dbsnp/{variantId}	Retrieves VEP annotation for the give dbSNP id
AnnotationControllerApi	FetchVariantAnnotationByIdPOST	Post /annotation/dbsnp/	Retrieves VEP annotation for the provided list of dbSNP ids
AnnotationControllerApi	FetchVariantAnnotationGET	Get /annotation/{variant}	Retrieves VEP annotation for the provided variant
AnnotationControllerApi	FetchVariantAnnotationPOST	Post /annotation	Retrieves VEP annotation for the provided list of variants
EnsemblControllerApi	FetchCanonicalEnsemblGeneIdByEntrezGeneIdGET	Get /ensembl/canonical-gene/entrez/{entrezGeneId}	Retrieves Ensembl canonical gene id by Entrez Gene Id
EnsemblControllerApi	FetchCanonicalEnsemblGeneIdByEntrezGeneIdsPOST	Post /ensembl/canonical-gene/entrez	Retrieves canonical Ensembl Gene ID by Entrez Gene Ids
EnsemblControllerApi	FetchCanonicalEnsemblGeneIdByHugoSymbolGET	Get /ensembl/canonical-gene/hgnc/{hugoSymbol}	Retrieves Ensembl canonical gene id by Hugo Symbol
EnsemblControllerApi	FetchCanonicalEnsemblGeneIdByHugoSymbolsPOST	Post /ensembl/canonical-gene/hgnc	Retrieves canonical Ensembl Gene ID by Hugo Symbols
EnsemblControllerApi	FetchCanonicalEnsemblTranscriptByHugoSymbolGET	Get /ensembl/canonical-transcript/hgnc/{hugoSymbol}	Retrieves Ensembl canonical transcript by Hugo Symbol
EnsemblControllerApi	FetchCanonicalEnsemblTranscriptsByHugoSymbolsPOST	Post /ensembl/canonical-transcript/hgnc	Retrieves Ensembl canonical transcripts by Hugo Symbols
EnsemblControllerApi	FetchEnsemblTranscriptByTranscriptIdGET	Get /ensembl/transcript/{transcriptId}	Retrieves the transcript by an Ensembl transcript ID
EnsemblControllerApi	FetchEnsemblTranscriptsByEnsemblFilterPOST	Post /ensembl/transcript	Retrieves Ensembl Transcripts by Ensembl transcript IDs, hugo Symbols, protein IDs, or gene IDs
EnsemblControllerApi	FetchEnsemblTranscriptsGET	Get /ensembl/transcript	Retrieves Ensembl Transcripts by protein ID, and gene ID. Retrieves all transcripts in case no query parameter provided
EnsemblControllerApi	FetchGeneXrefsGET	Get /ensembl/xrefs	Perform lookups of Ensembl identifiers and retrieve their external references in other databases
InfoControllerApi	FetchVersionGET	Get /version	Retrieve Genome Nexus Version
PdbControllerApi	FetchPdbHeaderGET	Get /pdb/header/{pdbId}	Retrieves PDB header info by a PDB id
PdbControllerApi	FetchPdbHeaderPOST	Post /pdb/header	Retrieves PDB header info by a PDB id
PfamControllerApi	FetchPfamDomainsByAccessionGET	Get /pfam/domain/{pfamAccession}	Retrieves a PFAM domain by a PFAM domain ID
PfamControllerApi	FetchPfamDomainsByPfamAccessionPOST	Post /pfam/domain	Retrieves PFAM domains by PFAM domain accession IDs
PtmControllerApi	FetchPostTranslationalModificationsByPtmFilterPOST	Post /ptm/experimental	Retrieves PTM entries by Ensembl Transcript IDs
PtmControllerApi	FetchPostTranslationalModificationsGET	Get /ptm/experimental	Retrieves PTM entries by Ensembl Transcript ID

Documentation For Models

• AggregateSourceInfo
• AlleleCount
• AlleleFrequency
• AlleleNumber
• Alleles
• ArticleAbstract
• Citations
• ClinVar
• Clinvar
• ClinvarAnnotation
• ColocatedVariant
• Cosmic
• CountByTumorType
• Dbsnp
• Drug
• EnsemblFilter
• EnsemblGene
• EnsemblTranscript
• Exon
• Gene
• GeneXref
• GeneralPopulationStats
• GenomeNexusInfo
• GenomicLocation
• Gnomad
• Hg19
• Hg38
• Hgvs
• Homozygotes
• Hotspot
• HotspotAnnotation
• HrdScore
• Implication
• IndicatorQueryResp
• IndicatorQueryTreatment
• IntegerRange
• IntergenicConsequences
• MainType
• MutationAssessor
• MutationAssessorAnnotation
• MutationEffectResp
• Mutdb
• MyVariantInfo
• MyVariantInfoAnnotation
• NucleotideContext
• NucleotideContextAnnotation
• OncokbAnnotation
• PdbHeader
• PfamDomain
• PfamDomainRange
• PostTranslationalModification
• PtmAnnotation
• PtmFilter
• Query
• Rcv
• SignalAnnotation
• SignalMutation
• SignalPopulationStats
• Snpeff
• SourceVersionInfo
• StatsByTumorType
• TranscriptConsequence
• TranscriptConsequenceSummary
• TumorType
• UntranslatedRegion
• VEPInfo
• VariantAnnotation
• VariantAnnotationSummary
• Vcf
• Version
• Vues

Documentation For Authorization

Endpoints do not require authorization.

Documentation for Utility Methods

Due to the fact that model structure members are all pointers, this package contains a number of utility functions to easily obtain pointers to values of basic types. Each of these functions takes a value of the given basic type and returns a pointer to it:

• PtrBool
• PtrInt
• PtrInt32
• PtrInt64
• PtrFloat
• PtrFloat32
• PtrFloat64
• PtrString
• PtrTime

Author