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from typing import Any |
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from . import __version__ |
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# Set Ensembl REST URL |
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ensembl_default_url = "https://rest.ensembl.org" |
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# Ensembl API lookup table |
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# Specifies the functions relevant to the Ensembl REST server |
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ensembl_api_table: dict[str, Any] = { |
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# Archive |
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"getArchiveById": { |
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"doc": "Uses the given identifier to return its latest version", |
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"url": "/archive/id/{{id}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getArchiveByMultipleIds": { |
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"doc": "Retrieve the latest version for a set of identifiers", |
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"url": "/archive/id", |
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"method": "POST", |
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"content_type": "application/json", |
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"post_parameters": ["id"], |
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}, |
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# Comparative Genomics |
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"getCafeGeneTreeById": { |
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"doc": "Retrieves a cafe tree of the gene tree using the gene tree stable identifier", |
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"url": "/cafe/genetree/id/{{id}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getCafeGeneTreeMemberBySymbol": { |
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"doc": "Retrieves the cafe tree of the gene tree that contains the gene identified by a symbol", |
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"url": "/cafe/genetree/member/symbol/{{species}}/{{symbol}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getCafeGeneTreeMemberById": { |
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"doc": "Retrieves the cafe tree of the gene tree that contains the gene / transcript / translation stable identifier in the given species", |
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"url": "/cafe/genetree/member/id/{{species}}/{{id}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getGeneTreeById": { |
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"doc": "Retrieves a gene tree for a gene tree stable identifier", |
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"url": "/genetree/id/{{id}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getGeneTreeMemberBySymbol": { |
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"doc": "Retrieves the gene tree that contains the gene identified by a symbol", |
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"url": "/genetree/member/symbol/{{species}}/{{symbol}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getGeneTreeMemberById": { |
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"doc": "Retrieves the gene tree that contains the gene / transcript / translation stable identifier in the given species", |
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"url": "/genetree/member/id/{{species}}/{{id}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getAlignmentByRegion": { |
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"doc": "Retrieves genomic alignments as separate blocks based on a region and species", |
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"url": "/alignment/region/{{species}}/{{region}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getHomologyById": { |
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"doc": "Retrieves homology information (orthologs) by species and Ensembl gene id", |
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"url": "/homology/id/{{species}}/{{id}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getHomologyBySymbol": { |
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"doc": "Retrieves homology information (orthologs) by symbol", |
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"url": "/homology/symbol/{{species}}/{{symbol}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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# Cross References |
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"getXrefsBySymbol": { |
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"doc": """Looks up an external symbol and returns all Ensembl objects linked to it. """ |
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"""This can be a display name for a gene/transcript/translation, """ |
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"""a synonym or an externally linked reference. """ |
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"""If a gene's transcript is linked to the supplied symbol """ |
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"""the service will return both gene and transcript (it supports transient links).""", |
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"url": "/xrefs/symbol/{{species}}/{{symbol}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getXrefsById": { |
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"doc": "Perform lookups of Ensembl Identifiers and retrieve their external references in other databases", |
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"url": "/xrefs/id/{{id}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getXrefsByName": { |
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"doc": """Performs a lookup based upon the primary accession or display label of an external reference """ |
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"""and returning the information we hold about the entry""", |
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"url": "/xrefs/name/{{species}}/{{name}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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# Information |
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"getInfoAnalysis": { |
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"doc": "List the names of analyses involved in generating Ensembl data.", |
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"url": "/info/analysis/{{species}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoAssembly": { |
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"doc": """List the currently available assemblies for a species, along with toplevel sequences, """ |
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"""chromosomes and cytogenetic bands.""", |
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"url": "/info/assembly/{{species}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoAssemblyRegion": { |
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"doc": "Returns information about the specified toplevel sequence region for the given species.", |
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"url": "/info/assembly/{{species}}/{{region_name}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoBiotypes": { |
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"doc": """List the functional classifications of gene models that Ensembl associates with a particular species. """ |
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"""Useful for restricting the type of genes/transcripts retrieved by other endpoints.""", |
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"url": "/info/biotypes/{{species}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoBiotypesByGroup": { |
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"doc": """Without argument the list of available biotype groups is returned. With :group argument provided, list the properties of biotypes within that group. """ |
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"""Object type (gene or transcript) can be provided for filtering.""", |
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"url": "/info/biotypes/groups/{{group}}/{{object_type}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoBiotypesByName": { |
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"doc": """List the properties of biotypes with a given name. """ |
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"""Object type (gene or transcript) can be provided for filtering.""", |
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"url": "/info/biotypes/name/{{name}}/{{object_type}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoComparaMethods": { |
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"doc": "List all compara analyses available (an analysis defines the type of comparative data).", |
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"url": "/info/compara/methods", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoComparaSpeciesSets": { |
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"doc": "List all collections of species analysed with the specified compara method.", |
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"url": "/info/compara/species_sets/{{methods}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoComparas": { |
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"doc": """Lists all available comparative genomics databases and their data release. """ |
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"""DEPRECATED: use info/genomes/division instead.""", |
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"url": "/info/comparas", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoData": { |
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"doc": """Shows the data releases available on this REST server. """ |
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"""May return more than one release (unfrequent non-standard Ensembl configuration).""", |
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"url": "/info/data", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoEgVersion": { |
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"doc": "Returns the Ensembl Genomes version of the databases backing this service", |
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"url": "/info/eg_version", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoExternalDbs": { |
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"doc": "Lists all available external sources for a species.", |
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"url": "/info/external_dbs/{{species}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoDivisions": { |
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"doc": "Get list of all Ensembl divisions for which information is available", |
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"url": "/info/divisions", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoGenomesByName": { |
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"doc": "Find information about a given genome", |
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"url": "/info/genomes/{{name}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoGenomesByAccession": { |
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"doc": "Find information about genomes containing a specified INSDC accession", |
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"url": "/info/genomes/accession/{{accession}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoGenomesByAssembly": { |
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"doc": "Find information about a genome with a specified assembly", |
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"url": "/info/genomes/assembly/{{assembly_id}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoGenomesByDivision": { |
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"doc": "Find information about all genomes in a given division. May be large for Ensembl Bacteria.", |
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"url": "/info/genomes/division/{{division}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoGenomesByTaxonomy": { |
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"doc": "Find information about all genomes beneath a given node of the taxonomy", |
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"url": "/info/genomes/taxonomy/{{taxon_name}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoPing": { |
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"doc": "Checks if the service is alive.", |
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"url": "/info/ping", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoRest": { |
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"doc": "Shows the current version of the Ensembl REST API.", |
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"url": "/info/rest", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoSoftware": { |
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"doc": "Shows the current version of the Ensembl API used by the REST server.", |
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"url": "/info/software", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoSpecies": { |
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"doc": "Lists all available species, their aliases, available adaptor groups and data release.", |
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"url": "/info/species", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoVariationBySpecies": { |
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"doc": "List the variation sources used in Ensembl for a species.", |
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"url": "/info/variation/{{species}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoVariationConsequenceTypes": { |
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"doc": "Lists all variant consequence types.", |
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"url": "/info/variation/consequence_types", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoVariationPopulationIndividuals": { |
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"doc": "List all individuals for a population from a species", |
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"url": "/info/variation/populations/{{species}}/{{population_name}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getInfoVariationPopulations": { |
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"doc": "List all populations for a species", |
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"url": "/info/variation/populations/{{species}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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# Linkage Disequilibrium |
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"getLdId": { |
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"doc": """Computes and returns LD values between the given variant and all other variants """ |
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"""in a window centered around the given variant. The window size is set to 500 kb.""", |
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"url": "/ld/{{species}}/{{id}}/{{population_name}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getLdPairwise": { |
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"doc": "Computes and returns LD values between the given variants.", |
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"url": "/ld/{{species}}/pairwise/{{id1}}/{{id2}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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"getLdRegion": { |
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"doc": "Computes and returns LD values between all pairs of variants in the defined region.", |
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"url": "/ld/{{species}}/region/{{region}}/{{population_name}}", |
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"method": "GET", |
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"content_type": "application/json", |
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}, |
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# Lookup |
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288
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"getLookupById": { |
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"doc": "Find the species and database for a single identifier e.g. gene, transcript, protein", |
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"url": "/lookup/id/{{id}}", |
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"method": "GET", |
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292
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"content_type": "application/json", |
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}, |
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294
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"getLookupByMultipleIds": { |
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295
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"doc": """Find the species and database for several identifiers. """ |
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296
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"""IDs that are not found are returned with no data.""", |
|
297
|
|
|
"url": "/lookup/id", |
|
298
|
|
|
"method": "POST", |
|
299
|
|
|
"content_type": "application/json", |
|
300
|
|
|
"post_parameters": ["ids"], |
|
301
|
|
|
}, |
|
302
|
|
|
"getLookupBySymbol": { |
|
303
|
|
|
"doc": "Find the species and database for a symbol in a linked external database", |
|
304
|
|
|
"url": "/lookup/symbol/{{species}}/{{symbol}}", |
|
305
|
|
|
"method": "GET", |
|
306
|
|
|
"content_type": "application/json", |
|
307
|
|
|
}, |
|
308
|
|
|
"getLookupByMultipleSymbols": { |
|
309
|
|
|
"doc": """Find the species and database for a set of symbols in a linked external database. """ |
|
310
|
|
|
"""Unknown symbols are omitted from the response.""", |
|
311
|
|
|
"url": "/lookup/symbol/{{species}}", |
|
312
|
|
|
"method": "POST", |
|
313
|
|
|
"content_type": "application/json", |
|
314
|
|
|
"post_parameters": ["symbols"], |
|
315
|
|
|
}, |
|
316
|
|
|
# Mapping |
|
317
|
|
|
"getMapCdnaToRegion": { |
|
318
|
|
|
"doc": """Convert from cDNA coordinates to genomic coordinates. """ |
|
319
|
|
|
"""Output reflects forward orientation coordinates as returned from the Ensembl API.""", |
|
320
|
|
|
"url": "/map/cdna/{{id}}/{{region}}", |
|
321
|
|
|
"method": "GET", |
|
322
|
|
|
"content_type": "application/json", |
|
323
|
|
|
}, |
|
324
|
|
|
"getMapCdsToRegion": { |
|
325
|
|
|
"doc": """Convert from CDS coordinates to genomic coordinates. """ |
|
326
|
|
|
"""Output reflects forward orientation coordinates as returned from the Ensembl API.""", |
|
327
|
|
|
"url": "/map/cds/{{id}}/{{region}}", |
|
328
|
|
|
"method": "GET", |
|
329
|
|
|
"content_type": "application/json", |
|
330
|
|
|
}, |
|
331
|
|
|
"getMapAssemblyOneToTwo": { |
|
332
|
|
|
"doc": "Convert the co-ordinates of one assembly to another", |
|
333
|
|
|
"url": "/map/{{species}}/{{asm_one}}/{{region}}/{{asm_two}}", |
|
334
|
|
|
"method": "GET", |
|
335
|
|
|
"content_type": "application/json", |
|
336
|
|
|
}, |
|
337
|
|
|
"getMapTranslationToRegion": { |
|
338
|
|
|
"doc": """Convert from protein (translation) coordinates to genomic coordinates. """ |
|
339
|
|
|
"""Output reflects forward orientation coordinates as returned from the Ensembl API.""", |
|
340
|
|
|
"url": "/map/translation/{{id}}/{{region}}", |
|
341
|
|
|
"method": "GET", |
|
342
|
|
|
"content_type": "application/json", |
|
343
|
|
|
}, |
|
344
|
|
|
# Ontologies and Taxonomy |
|
345
|
|
|
"getAncestorsById": { |
|
346
|
|
|
"doc": "Reconstruct the entire ancestry of a term from is_a and part_of relationships", |
|
347
|
|
|
"url": "/ontology/ancestors/{{id}}", |
|
348
|
|
|
"method": "GET", |
|
349
|
|
|
"content_type": "application/json", |
|
350
|
|
|
}, |
|
351
|
|
|
"getAncestorsChartById": { |
|
352
|
|
|
"doc": "Reconstruct the entire ancestry of a term from is_a and part_of relationships.", |
|
353
|
|
|
"url": "/ontology/ancestors/chart/{{id}}", |
|
354
|
|
|
"method": "GET", |
|
355
|
|
|
"content_type": "application/json", |
|
356
|
|
|
}, |
|
357
|
|
|
"getDescendantsById": { |
|
358
|
|
|
"doc": """Find all the terms descended from a given term. """ |
|
359
|
|
|
"""By default searches are conducted within the namespace of the given identifier""", |
|
360
|
|
|
"url": "/ontology/descendants/{{id}}", |
|
361
|
|
|
"method": "GET", |
|
362
|
|
|
"content_type": "application/json", |
|
363
|
|
|
}, |
|
364
|
|
|
"getOntologyById": { |
|
365
|
|
|
"doc": "Search for an ontological term by its namespaced identifier", |
|
366
|
|
|
"url": "/ontology/id/{{id}}", |
|
367
|
|
|
"method": "GET", |
|
368
|
|
|
"content_type": "application/json", |
|
369
|
|
|
}, |
|
370
|
|
|
"getOntologyByName": { |
|
371
|
|
|
"doc": "Search for a list of ontological terms by their name", |
|
372
|
|
|
"url": "/ontology/name/{{name}}", |
|
373
|
|
|
"method": "GET", |
|
374
|
|
|
"content_type": "application/json", |
|
375
|
|
|
}, |
|
376
|
|
|
"getTaxonomyClassificationById": { |
|
377
|
|
|
"doc": "Return the taxonomic classification of a taxon node", |
|
378
|
|
|
"url": "/taxonomy/classification/{{id}}", |
|
379
|
|
|
"method": "GET", |
|
380
|
|
|
"content_type": "application/json", |
|
381
|
|
|
}, |
|
382
|
|
|
"getTaxonomyById": { |
|
383
|
|
|
"doc": "Search for a taxonomic term by its identifier or name", |
|
384
|
|
|
"url": "/taxonomy/id/{{id}}", |
|
385
|
|
|
"method": "GET", |
|
386
|
|
|
"content_type": "application/json", |
|
387
|
|
|
}, |
|
388
|
|
|
"getTaxonomyByName": { |
|
389
|
|
|
"doc": "Search for a taxonomic id by a non-scientific name", |
|
390
|
|
|
"url": "/taxonomy/name/{{name}}", |
|
391
|
|
|
"method": "GET", |
|
392
|
|
|
"content_type": "application/json", |
|
393
|
|
|
}, |
|
394
|
|
|
# Overlap |
|
395
|
|
|
"getOverlapById": { |
|
396
|
|
|
"doc": """Retrieves features (e.g. genes, transcripts, variants and more) """ |
|
397
|
|
|
"""that overlap a region defined by the given identifier.""", |
|
398
|
|
|
"url": "/overlap/id/{{id}}", |
|
399
|
|
|
"method": "GET", |
|
400
|
|
|
"content_type": "application/json", |
|
401
|
|
|
}, |
|
402
|
|
|
"getOverlapByRegion": { |
|
403
|
|
|
"doc": """Retrieves features (e.g. genes, transcripts, variants and more) """ |
|
404
|
|
|
"""that overlap a given region.""", |
|
405
|
|
|
"url": "/overlap/region/{{species}}/{{region}}", |
|
406
|
|
|
"method": "GET", |
|
407
|
|
|
"content_type": "application/json", |
|
408
|
|
|
}, |
|
409
|
|
|
"getOverlapByTranslation": { |
|
410
|
|
|
"doc": """Retrieve features related to a specific Translation as described """ |
|
411
|
|
|
"""by its stable ID (e.g. domains, variants).""", |
|
412
|
|
|
"url": "/overlap/translation/{{id}}", |
|
413
|
|
|
"method": "GET", |
|
414
|
|
|
"content_type": "application/json", |
|
415
|
|
|
}, |
|
416
|
|
|
# Phenotype annotations |
|
417
|
|
|
"getPhenotypeByAccession": { |
|
418
|
|
|
"doc": "Return phenotype annotations for genomic features given a phenotype ontology accession", |
|
419
|
|
|
"url": "/phenotype/accession/{{species}}/{{accession}}", |
|
420
|
|
|
"method": "GET", |
|
421
|
|
|
"content_type": "application/json", |
|
422
|
|
|
}, |
|
423
|
|
|
"getPhenotypeByGene": { |
|
424
|
|
|
"doc": "Return phenotype annotations for a given gene.", |
|
425
|
|
|
"url": "/phenotype/gene/{{species}}/{{gene}}", |
|
426
|
|
|
"method": "GET", |
|
427
|
|
|
"content_type": "application/json", |
|
428
|
|
|
}, |
|
429
|
|
|
"getPhenotypeByRegion": { |
|
430
|
|
|
"doc": "Return phenotype annotations that overlap a given genomic region.", |
|
431
|
|
|
"url": "/phenotype/region/{{species}}/{{region}}", |
|
432
|
|
|
"method": "GET", |
|
433
|
|
|
"content_type": "application/json", |
|
434
|
|
|
}, |
|
435
|
|
|
"getPhenotypeByTerm": { |
|
436
|
|
|
"doc": "Return phenotype annotations for genomic features given a phenotype ontology term", |
|
437
|
|
|
"url": "/phenotype/term/{{species}}/{{term}}", |
|
438
|
|
|
"method": "GET", |
|
439
|
|
|
"content_type": "application/json", |
|
440
|
|
|
}, |
|
441
|
|
|
# Regulation |
|
442
|
|
|
"getRegulationBindingMatrix": { |
|
443
|
|
|
"doc": "Return the specified binding matrix", |
|
444
|
|
|
"url": "/species/{{species}}/binding_matrix/{{binding_matrix}}/", |
|
445
|
|
|
"method": "GET", |
|
446
|
|
|
"content_type": "application/json", |
|
447
|
|
|
}, |
|
448
|
|
|
# Sequences |
|
449
|
|
|
"getSequenceById": { |
|
450
|
|
|
"doc": """Request multiple types of sequence by stable identifier. """ |
|
451
|
|
|
"""Supports feature masking and expand options.""", |
|
452
|
|
|
"url": "/sequence/id/{{id}}", |
|
453
|
|
|
"method": "GET", |
|
454
|
|
|
"content_type": "application/json", |
|
455
|
|
|
}, |
|
456
|
|
|
"getSequenceByMultipleIds": { |
|
457
|
|
|
"doc": "Request multiple types of sequence by a stable identifier list.", |
|
458
|
|
|
"url": "/sequence/id", |
|
459
|
|
|
"method": "POST", |
|
460
|
|
|
"content_type": "application/json", |
|
461
|
|
|
"post_parameters": ["ids"], |
|
462
|
|
|
}, |
|
463
|
|
|
"getSequenceByRegion": { |
|
464
|
|
|
"doc": """Returns the genomic sequence of the specified region of the given species. """ |
|
465
|
|
|
"""Supports feature masking and expand options.""", |
|
466
|
|
|
"url": "/sequence/region/{{species}}/{{region}}", |
|
467
|
|
|
"method": "GET", |
|
468
|
|
|
"content_type": "application/json", |
|
469
|
|
|
}, |
|
470
|
|
|
"getSequenceByMultipleRegions": { |
|
471
|
|
|
"doc": "Request multiple types of sequence by a list of regions.", |
|
472
|
|
|
"url": "/sequence/region/{{species}}", |
|
473
|
|
|
"method": "POST", |
|
474
|
|
|
"content_type": "application/json", |
|
475
|
|
|
"post_parameters": ["regions"], |
|
476
|
|
|
}, |
|
477
|
|
|
# Transcript Haplotypes |
|
478
|
|
|
"getTranscriptHaplotypes": { |
|
479
|
|
|
"doc": "Computes observed transcript haplotype sequences based on phased genotype data", |
|
480
|
|
|
"url": "/transcript_haplotypes/{{species}}/{{id}}", |
|
481
|
|
|
"method": "GET", |
|
482
|
|
|
"content_type": "application/json", |
|
483
|
|
|
}, |
|
484
|
|
|
# VEP |
|
485
|
|
|
"getVariantConsequencesByHGVSNotation": { |
|
486
|
|
|
"doc": "Fetch variant consequences based on a HGVS notation", |
|
487
|
|
|
"url": "/vep/{{species}}/hgvs/{{hgvs_notation}}", |
|
488
|
|
|
"method": "GET", |
|
489
|
|
|
"content_type": "application/json", |
|
490
|
|
|
}, |
|
491
|
|
|
"getVariantConsequencesByMultipleHGVSNotations": { |
|
492
|
|
|
"doc": "Fetch variant consequences for multiple HGVS notations", |
|
493
|
|
|
"url": "/vep/{{species}}/hgvs/", |
|
494
|
|
|
"method": "POST", |
|
495
|
|
|
"content_type": "application/json", |
|
496
|
|
|
"post_parameters": ["hgvs_notations"], |
|
497
|
|
|
}, |
|
498
|
|
|
"getVariantConsequencesById": { |
|
499
|
|
|
"doc": "Fetch variant consequences based on a variant identifier", |
|
500
|
|
|
"url": "/vep/{{species}}/id/{{id}}", |
|
501
|
|
|
"method": "GET", |
|
502
|
|
|
"content_type": "application/json", |
|
503
|
|
|
}, |
|
504
|
|
|
"getVariantConsequencesByMultipleIds": { |
|
505
|
|
|
"doc": "Fetch variant consequences for multiple ids", |
|
506
|
|
|
"url": "/vep/{{species}}/id", |
|
507
|
|
|
"method": "POST", |
|
508
|
|
|
"content_type": "application/json", |
|
509
|
|
|
"post_parameters": ["ids"], |
|
510
|
|
|
}, |
|
511
|
|
|
"getVariantConsequencesByRegion": { |
|
512
|
|
|
"doc": "Fetch variant consequences", |
|
513
|
|
|
"url": "/vep/{{species}}/region/{{region}}/{{allele}}", |
|
514
|
|
|
"method": "GET", |
|
515
|
|
|
"content_type": "application/json", |
|
516
|
|
|
}, |
|
517
|
|
|
"getVariantConsequencesByMultipleRegions": { |
|
518
|
|
|
"doc": "Fetch variant consequences for multiple regions", |
|
519
|
|
|
"url": "/vep/{{species}}/region", |
|
520
|
|
|
"method": "POST", |
|
521
|
|
|
"content_type": "application/json", |
|
522
|
|
|
"post_parameters": ["variants"], |
|
523
|
|
|
}, |
|
524
|
|
|
# Variation |
|
525
|
|
|
"getVariationRecoderById": { |
|
526
|
|
|
"doc": """Translate a variant identifier, HGVS notation or genomic SPDI notation """ |
|
527
|
|
|
"""to all possible variant IDs, HGVS and genomic SPDI""", |
|
528
|
|
|
"url": "/variant_recoder/{{species}}/{{id}}", |
|
529
|
|
|
"method": "GET", |
|
530
|
|
|
"content_type": "application/json", |
|
531
|
|
|
}, |
|
532
|
|
|
"getVariationRecoderByMultipleIds": { |
|
533
|
|
|
"doc": """Translate a list of variant identifiers, HGVS notations or genomic SPDI """ |
|
534
|
|
|
"""notations to all possible variant IDs, HGVS and genomic SPDI""", |
|
535
|
|
|
"url": "/variant_recoder/{{species}}", |
|
536
|
|
|
"method": "POST", |
|
537
|
|
|
"content_type": "application/json", |
|
538
|
|
|
"post_parameters": ["ids"], |
|
539
|
|
|
}, |
|
540
|
|
|
"getVariationById": { |
|
541
|
|
|
"doc": """Uses a variant identifier (e.g. rsID) to return the variation features """ |
|
542
|
|
|
"""including optional genotype, phenotype and population data""", |
|
543
|
|
|
"url": "/variation/{{species}}/{{id}}", |
|
544
|
|
|
"method": "GET", |
|
545
|
|
|
"content_type": "application/json", |
|
546
|
|
|
}, |
|
547
|
|
|
"getVariationByPMCID": { |
|
548
|
|
|
"doc": """Uses a variant identifier (e.g. rsID) to return the variation features """ |
|
549
|
|
|
"""including optional genotype, phenotype and population data""", |
|
550
|
|
|
"url": "/variation/{{species}}/pmcid/{{pmcid}}", |
|
551
|
|
|
"method": "GET", |
|
552
|
|
|
"content_type": "application/json", |
|
553
|
|
|
}, |
|
554
|
|
|
"getVariationByPMID": { |
|
555
|
|
|
"doc": """Uses a variant identifier (e.g. rsID) to return the variation features """ |
|
556
|
|
|
"""including optional genotype, phenotype and population data""", |
|
557
|
|
|
"url": "/variation/{{species}}/pmid/{{pmid}}", |
|
558
|
|
|
"method": "GET", |
|
559
|
|
|
"content_type": "application/json", |
|
560
|
|
|
}, |
|
561
|
|
|
"getVariationByMultipleIds": { |
|
562
|
|
|
"doc": """Uses a list of variant identifiers (e.g. rsID) to return the variation features """ |
|
563
|
|
|
"""including optional genotype, phenotype and population data """, |
|
564
|
|
|
"url": "/variation/{{species}}", |
|
565
|
|
|
"method": "POST", |
|
566
|
|
|
"content_type": "application/json", |
|
567
|
|
|
"post_parameters": ["ids"], |
|
568
|
|
|
}, |
|
569
|
|
|
# Variation GA4GH |
|
570
|
|
|
"getGA4GHBeacon": { |
|
571
|
|
|
"doc": "Return Beacon information", |
|
572
|
|
|
"url": "/ga4gh/beacon", |
|
573
|
|
|
"method": "GET", |
|
574
|
|
|
"content_type": "application/json", |
|
575
|
|
|
}, |
|
576
|
|
|
"getGA4GHBeaconQuery": { |
|
577
|
|
|
"doc": "Return the Beacon response for allele information", |
|
578
|
|
|
"url": "/ga4gh/beacon/query?" |
|
579
|
|
|
"alternateBases={{alternateBases}};" |
|
580
|
|
|
"assemblyId={{assemblyId}};" |
|
581
|
|
|
"referenceBases={{referenceBases}};" |
|
582
|
|
|
"referenceName={{referenceName}};" |
|
583
|
|
|
"start={{start}}", |
|
584
|
|
|
"method": "GET", |
|
585
|
|
|
"content_type": "application/json", |
|
586
|
|
|
}, |
|
587
|
|
|
"postGA4GHBeaconQuery": { |
|
588
|
|
|
"doc": "Return the Beacon response for allele information", |
|
589
|
|
|
"url": "/ga4gh/beacon/query", |
|
590
|
|
|
"method": "POST", |
|
591
|
|
|
"content_type": "application/json", |
|
592
|
|
|
"post_parameters": [ |
|
593
|
|
|
"alternateBases", |
|
594
|
|
|
"assemblyId", |
|
595
|
|
|
"end", |
|
596
|
|
|
"referenceBases", |
|
597
|
|
|
"referenceName", |
|
598
|
|
|
"start", |
|
599
|
|
|
"variantType", |
|
600
|
|
|
], |
|
601
|
|
|
}, |
|
602
|
|
|
"getGA4GHFeaturesById": { |
|
603
|
|
|
"doc": "Return the GA4GH record for a specific sequence feature given its identifier", |
|
604
|
|
|
"url": "/ga4gh/features/{{id}}", |
|
605
|
|
|
"method": "GET", |
|
606
|
|
|
"content_type": "application/json", |
|
607
|
|
|
}, |
|
608
|
|
|
"searchGA4GHFeatures": { |
|
609
|
|
|
"doc": "Return a list of sequence annotation features in GA4GH format", |
|
610
|
|
|
"url": "/ga4gh/features/search", |
|
611
|
|
|
"method": "POST", |
|
612
|
|
|
"content_type": "application/json", |
|
613
|
|
|
"post_parameters": [ |
|
614
|
|
|
"end", |
|
615
|
|
|
"referenceName", |
|
616
|
|
|
"start", |
|
617
|
|
|
"featureSetId", |
|
618
|
|
|
"parentId", |
|
619
|
|
|
], |
|
620
|
|
|
}, |
|
621
|
|
|
"searchGA4GHCallset": { |
|
622
|
|
|
"doc": "Return a list of sets of genotype calls for specific samples in GA4GH format", |
|
623
|
|
|
"url": "/ga4gh/callsets/search", |
|
624
|
|
|
"method": "POST", |
|
625
|
|
|
"content_type": "application/json", |
|
626
|
|
|
"post_parameters": ["variantSetId", "name", "pageToken", "pageSize"], |
|
627
|
|
|
}, |
|
628
|
|
|
"getGA4GHCallsetById": { |
|
629
|
|
|
"doc": "Return the GA4GH record for a specific CallSet given its identifier", |
|
630
|
|
|
"url": "/ga4gh/callsets/{{id}}", |
|
631
|
|
|
"method": "GET", |
|
632
|
|
|
"content_type": "application/json", |
|
633
|
|
|
}, |
|
634
|
|
|
"searchGA4GHDatasets": { |
|
635
|
|
|
"doc": "Return a list of datasets in GA4GH format", |
|
636
|
|
|
"url": "/ga4gh/datasets/search", |
|
637
|
|
|
"method": "POST", |
|
638
|
|
|
"content_type": "application/json", |
|
639
|
|
|
"post_parameters": ["pageToken", "pageSize"], |
|
640
|
|
|
}, |
|
641
|
|
|
"getGA4GHDatasetsById": { |
|
642
|
|
|
"doc": "Return the GA4GH record for a specific dataset given its identifier", |
|
643
|
|
|
"url": "/ga4gh/datasets/{{id}}", |
|
644
|
|
|
"method": "GET", |
|
645
|
|
|
"content_type": "application/json", |
|
646
|
|
|
}, |
|
647
|
|
|
"searchGA4GHFeaturesets": { |
|
648
|
|
|
"doc": "Return a list of feature sets in GA4GH format", |
|
649
|
|
|
"url": "/ga4gh/featuresets/search", |
|
650
|
|
|
"method": "POST", |
|
651
|
|
|
"content_type": "application/json", |
|
652
|
|
|
"post_parameters": ["datasetId", "pageToken", "pageSize"], |
|
653
|
|
|
}, |
|
654
|
|
|
"getGA4GHFeaturesetsById": { |
|
655
|
|
|
"doc": "Return the GA4GH record for a specific featureSet given its identifier", |
|
656
|
|
|
"url": "/ga4gh/featuresets/{{id}}", |
|
657
|
|
|
"method": "GET", |
|
658
|
|
|
"content_type": "application/json", |
|
659
|
|
|
}, |
|
660
|
|
|
"getGA4GHVariantsById": { |
|
661
|
|
|
"doc": "Return the GA4GH record for a specific variant given its identifier.", |
|
662
|
|
|
"url": "/ga4gh/variants/{{id}}", |
|
663
|
|
|
"method": "GET", |
|
664
|
|
|
"content_type": "application/json", |
|
665
|
|
|
}, |
|
666
|
|
|
"searchGA4GHVariantAnnotations": { |
|
667
|
|
|
"doc": "Return variant annotation information in GA4GH format for a region on a reference sequence", |
|
668
|
|
|
"url": "/ga4gh/variantannotations/search", |
|
669
|
|
|
"method": "POST", |
|
670
|
|
|
"content_type": "application/json", |
|
671
|
|
|
"post_parameters": [ |
|
672
|
|
|
"variantAnnotationSetId", |
|
673
|
|
|
"effects", |
|
674
|
|
|
"end", |
|
675
|
|
|
"pageSize", |
|
676
|
|
|
"pageToken", |
|
677
|
|
|
"referenceId", |
|
678
|
|
|
"referenceName", |
|
679
|
|
|
"start", |
|
680
|
|
|
], |
|
681
|
|
|
}, |
|
682
|
|
|
"searchGA4GHVariants": { |
|
683
|
|
|
"doc": "Return variant call information in GA4GH format for a region on a reference sequence", |
|
684
|
|
|
"url": "/ga4gh/variants/search", |
|
685
|
|
|
"method": "POST", |
|
686
|
|
|
"content_type": "application/json", |
|
687
|
|
|
"post_parameters": [ |
|
688
|
|
|
"variantSetId", |
|
689
|
|
|
"callSetIds", |
|
690
|
|
|
"referenceName", |
|
691
|
|
|
"start", |
|
692
|
|
|
"end", |
|
693
|
|
|
"pageToken", |
|
694
|
|
|
"pageSize", |
|
695
|
|
|
], |
|
696
|
|
|
}, |
|
697
|
|
|
"searchGA4GHVariantsets": { |
|
698
|
|
|
"doc": "Return a list of variant sets in GA4GH format", |
|
699
|
|
|
"url": "/ga4gh/variantsets/search", |
|
700
|
|
|
"method": "POST", |
|
701
|
|
|
"content_type": "application/json", |
|
702
|
|
|
"post_parameters": ["datasetId", "pageToken", "pageSize"], |
|
703
|
|
|
}, |
|
704
|
|
|
"getGA4GHVariantsetsById": { |
|
705
|
|
|
"doc": "Return the GA4GH record for a specific VariantSet given its identifier", |
|
706
|
|
|
"url": "/ga4gh/variantsets/{{id}}", |
|
707
|
|
|
"method": "GET", |
|
708
|
|
|
"content_type": "application/json", |
|
709
|
|
|
}, |
|
710
|
|
|
"searchGA4GHReferences": { |
|
711
|
|
|
"doc": "Return a list of reference sequences in GA4GH format", |
|
712
|
|
|
"url": "/ga4gh/references/search", |
|
713
|
|
|
"method": "POST", |
|
714
|
|
|
"content_type": "application/json", |
|
715
|
|
|
"post_parameters": [ |
|
716
|
|
|
"referenceSetId", |
|
717
|
|
|
"md5checksum", |
|
718
|
|
|
"accession", |
|
719
|
|
|
"pageToken", |
|
720
|
|
|
"pageSize", |
|
721
|
|
|
], |
|
722
|
|
|
}, |
|
723
|
|
|
"getGA4GHReferencesById": { |
|
724
|
|
|
"doc": "Return data for a specific reference in GA4GH format by id", |
|
725
|
|
|
"url": "/ga4gh/references/{{id}}", |
|
726
|
|
|
"method": "GET", |
|
727
|
|
|
"content_type": "application/json", |
|
728
|
|
|
}, |
|
729
|
|
|
"searchGA4GHReferencesets": { |
|
730
|
|
|
"doc": "Return a list of reference sets in GA4GH format", |
|
731
|
|
|
"url": "/ga4gh/referencesets/search", |
|
732
|
|
|
"method": "POST", |
|
733
|
|
|
"content_type": "application/json", |
|
734
|
|
|
"post_parameters": ["accession", "pageToken", "pageSize"], |
|
735
|
|
|
}, |
|
736
|
|
|
"getGA4GHReferencesetsById": { |
|
737
|
|
|
"doc": "Return data for a specific reference set in GA4GH format", |
|
738
|
|
|
"url": "/ga4gh/referencesets/{{id}}", |
|
739
|
|
|
"method": "GET", |
|
740
|
|
|
"content_type": "application/json", |
|
741
|
|
|
}, |
|
742
|
|
|
"searchGA4GHVariantAnnotationsets": { |
|
743
|
|
|
"doc": "Return a list of annotation sets in GA4GH format", |
|
744
|
|
|
"url": "/ga4gh/variantannotationsets/search", |
|
745
|
|
|
"method": "POST", |
|
746
|
|
|
"content_type": "application/json", |
|
747
|
|
|
"post_parameters": ["variantSetId", "pageToken", "pageSize"], |
|
748
|
|
|
}, |
|
749
|
|
|
"getGA4GHVariantAnnotationsetsById": { |
|
750
|
|
|
"doc": "Return meta data for a specific annotation set in GA4GH format", |
|
751
|
|
|
"url": "/ga4gh/variantannotationsets/{{id}}", |
|
752
|
|
|
"method": "GET", |
|
753
|
|
|
"content_type": "application/json", |
|
754
|
|
|
}, |
|
755
|
|
|
} |
|
756
|
|
|
|
|
757
|
|
|
# Define HTTP status codes |
|
758
|
|
|
ensembl_http_status_codes: dict[int, Any] = { |
|
759
|
|
|
200: ( |
|
760
|
|
|
"OK", |
|
761
|
|
|
"Request was a success. Only process data from the service when you receive this code", |
|
762
|
|
|
), |
|
763
|
|
|
400: ( |
|
764
|
|
|
"Bad Request", |
|
765
|
|
|
"Occurs during exceptional circumstances such as the service is unable to find an ID. " |
|
766
|
|
|
"Check if the response Content-type or Accept was JSON. " |
|
767
|
|
|
"If so the JSON object is an exception hash with the message keyed under error", |
|
768
|
|
|
), |
|
769
|
|
|
403: ( |
|
770
|
|
|
"Forbidden", |
|
771
|
|
|
"You are submitting far too many requests and have been temporarily forbidden access to the service. " |
|
772
|
|
|
"Wait and retry with a maximum of 15 requests per second.", |
|
773
|
|
|
), |
|
774
|
|
|
404: ("Not Found", "Indicates a badly formatted request. Check your URL"), |
|
775
|
|
|
408: ("Timeout", "The request was not processed in time. Wait and retry later"), |
|
776
|
|
|
415: ( |
|
777
|
|
|
"Unsupported Media Type", |
|
778
|
|
|
"The server is refusing to service the request " |
|
779
|
|
|
"because the entity of the request is in a format not supported " |
|
780
|
|
|
"by the requested resource for the requested method", |
|
781
|
|
|
), |
|
782
|
|
|
429: ( |
|
783
|
|
|
"Too Many Requests", |
|
784
|
|
|
"You have been rate-limited; wait and retry. " |
|
785
|
|
|
"The headers X-RateLimit-Reset, X-RateLimit-Limit and X-RateLimit-Remaining will inform you " |
|
786
|
|
|
"of how long you have until your limit is reset and what that limit was. " |
|
787
|
|
|
"If you get this response and have not exceeded your limit then check " |
|
788
|
|
|
"if you have made too many requests per second.", |
|
789
|
|
|
), |
|
790
|
|
|
500: ( |
|
791
|
|
|
"Internal Server Error", |
|
792
|
|
|
"This error is not documented. Maybe there is an error in user input or " |
|
793
|
|
|
"the REST server could have problems. Try to do the query with curl. " |
|
794
|
|
|
"If your data input and query are correct, contact the Ensembl team", |
|
795
|
|
|
), |
|
796
|
|
|
503: ( |
|
797
|
|
|
"Service Unavailable", |
|
798
|
|
|
"The service is temporarily down; retry after a pause", |
|
799
|
|
|
), |
|
800
|
|
|
} |
|
801
|
|
|
|
|
802
|
|
|
# Set the user agent |
|
803
|
|
|
ensembl_user_agent = "pyEnsemblRest v" + __version__ |
|
804
|
|
|
ensembl_header = {"User-Agent": ensembl_user_agent} |
|
805
|
|
|
ensembl_content_type = "application/json" |
|
806
|
|
|
|
|
807
|
|
|
# Define known errors |
|
808
|
|
|
ensembl_known_errors = [ |
|
809
|
|
|
"something bad has happened", |
|
810
|
|
|
"Something went wrong while fetching from LDFeatureContainerAdaptor", |
|
811
|
|
|
"%s timeout" % ensembl_user_agent, |
|
812
|
|
|
] |
|
813
|
|
|
|
gawbul /
pyEnsemblRest
