igvf-catalog-client
Python client for the IGVF Catalog API.
IGVF Catalog OpenAPI compliant REST API built using tRPC with Express.
Our database uses 0-based, half-open coordinates for genomic coordinates in the GRCh38 (human) and GRCm39 (mouse) reference genomes.
Data is licensed under the <a href=https://creativecommons.org/licenses/by/4.0/ target="_blank">Creative Commons license and the software is licensed under the <a href=https://spdx.org/licenses/MIT.html target="_blank">MIT license.
- API version: 1.3.0
- Package version: 1.3.0
- Generator version: 7.14.0
This package is generated with OpenAPI Generator by
igvf-catalog-client-openapi-spec
whenever the IGVF Catalog changes. Don't edit generated files by hand; change
templates/ here or the pipeline in that repo instead.
Requirements
Python 3.9+
Installation
Releases follow IGVF Catalog releases and are published to PyPI:
pip install igvf-catalog-client
Development builds track the catalog's dev branch and are installed from this repo's dev branch:
pip install "git+https://github.com/IGVF-DACC/igvf-catalog-python-client.git@dev"
The default host is the API the package was generated against: releases use
https://api.catalogkg.igvf.org/api and dev builds use
https://catalog-api-dev.demo.igvf.org/api. Pass Configuration(host=...) to use another.
Quick start
import igvf_catalog_client
configuration = igvf_catalog_client.Configuration(host="https://api.catalogkg.igvf.org/api")
with igvf_catalog_client.ApiClient(configuration) as api_client:
api = igvf_catalog_client.IgvfCatalogApi(api_client)
genes = api.genes(name="ATF3")
print(genes[0].to_dict())
Every endpoint is a method on IgvfCatalogApi, listed below. The interactive API documentation is at
api.catalogkg.igvf.org.
Getting Started
import igvf_catalog_client
from igvf_catalog_client.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to https://api.catalogkg.igvf.org/api
# See configuration.py for a list of all supported configuration parameters.
configuration = igvf_catalog_client.Configuration(
host = "https://api.catalogkg.igvf.org/api"
)
# Enter a context with an instance of the API client
with igvf_catalog_client.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = igvf_catalog_client.IgvfCatalogApi(api_client)
gene_id = 'gene_id_example' # str |
dataset = 'dataset_example' # str |
page = 0 # float | (optional) (default to 0)
limit = 3.4 # float | (optional)
try:
api_response = api_instance.all_coding_variants_from_genes(gene_id, dataset, page=page, limit=limit)
print("The response of IgvfCatalogApi->all_coding_variants_from_genes:\n")
pprint(api_response)
except ApiException as e:
print("Exception when calling IgvfCatalogApi->all_coding_variants_from_genes: %s\n" % e)
Documentation for API Endpoints
All URIs are relative to https://api.catalogkg.igvf.org/api
| Class | Method | HTTP request | Description |
|---|---|---|---|
| IgvfCatalogApi | variants | GET /variants | |
| IgvfCatalogApi | coding_variants | GET /coding-variants | |
| IgvfCatalogApi | genomic_elements | GET /genomic-elements | |
| IgvfCatalogApi | genes | GET /genes | |
| IgvfCatalogApi | genes_structure | GET /genes-structure | |
| IgvfCatalogApi | transcripts | GET /transcripts | |
| IgvfCatalogApi | proteins | GET /proteins | |
| IgvfCatalogApi | complexes | GET /complexes | |
| IgvfCatalogApi | pathways | GET /pathways | |
| IgvfCatalogApi | motifs | GET /motifs | |
| IgvfCatalogApi | drugs | GET /drugs | |
| IgvfCatalogApi | ontology_term | GET /ontology-terms | |
| IgvfCatalogApi | studies | GET /studies | |
| IgvfCatalogApi | genomic_elements_from_variants | GET /variants/genomic-elements | |
| IgvfCatalogApi | genes_from_variants | GET /variants/genes | |
| IgvfCatalogApi | proteins_from_variants | GET /variants/proteins | |
| IgvfCatalogApi | phenotypes_from_variants | GET /variants/phenotypes | |
| IgvfCatalogApi | biosamples_from_variants | GET /variants/biosamples | |
| IgvfCatalogApi | variants_from_proteins | GET /proteins/variants | |
| IgvfCatalogApi | proteins_proteins | GET /proteins/proteins | |
| IgvfCatalogApi | variants_from_phenotypes | GET /phenotypes/variants | |
| IgvfCatalogApi | coding_variants_from_phenotypes | GET /phenotypes/coding-variants | |
| IgvfCatalogApi | genomic_elements_from_phenotypes | GET /phenotypes/genomic-elements | |
| IgvfCatalogApi | variants_from_genomic_elements | GET /genomic-elements/variants | |
| IgvfCatalogApi | genes_from_genomic_elements | GET /genomic-elements/genes | |
| IgvfCatalogApi | phenotypes_from_genomic_elements | GET /genomic-elements/phenotypes | |
| IgvfCatalogApi | biosamples_from_genomic_elements | GET /genomic-elements/biosamples | |
| IgvfCatalogApi | genomic_elements_from_genomic_elements | GET /genomic-elements/genomic-elements | |
| IgvfCatalogApi | variants_from_genes | GET /genes/variants | |
| IgvfCatalogApi | genomic_elements_from_genes | GET /genes/genomic-elements | |
| IgvfCatalogApi | phenotypes_from_coding_variants | GET /coding-variants/phenotypes | |
| IgvfCatalogApi | variants_from_biosamples | GET /biosamples/variants | |
| IgvfCatalogApi | genomic_elements_from_biosamples | GET /biosamples/genomic-elements | |
| IgvfCatalogApi | variant_by_frequency_source | GET /variants/freq | |
| IgvfCatalogApi | grn | GET /gene-regulatory-network | |
| IgvfCatalogApi | enhancer_gene_predictions | GET /enhancer-gene-predictions | |
| IgvfCatalogApi | qtls | GET /qtls | |
| IgvfCatalogApi | variant_summary | GET /variants/summary | |
| IgvfCatalogApi | variants_from_variant_id_summary | GET /variants/variant-ld/summary | |
| IgvfCatalogApi | variants_region_summary | GET /variants/region-summary | |
| IgvfCatalogApi | qtl_summary_endpoint | GET /variants/genes/summary | |
| IgvfCatalogApi | genomic_elements_from_variants_count | GET /variants/predictions-count | |
| IgvfCatalogApi | predictions_from_variants | GET /variants/predictions | |
| IgvfCatalogApi | deprecated_coding_variants_summary | GET /variants/phenotypes/score-summary | |
| IgvfCatalogApi | nearest_genes | GET /variants/nearest-genes | |
| IgvfCatalogApi | variants_alleles | GET /variants/gnomad-alleles | |
| IgvfCatalogApi | variants_genomic_elements_genes | GET /variants/genomic-elements/genes | |
| IgvfCatalogApi | genomic_elements_predictions_from_variant | GET /variants/genomic-elements/cell-gene-predictions | |
| IgvfCatalogApi | genes_proteins_from_variants | GET /variants/genes-proteins | |
| IgvfCatalogApi | coding_variants_from_genes | GET /genes/coding-variants/scores | |
| IgvfCatalogApi | all_coding_variants_from_genes | GET /genes/coding-variants/all-scores | |
| IgvfCatalogApi | variants_from_gene_proteins | GET /genes-proteins/variants | |
| IgvfCatalogApi | genes_proteins_genes_proteins | GET /genes-proteins/genes-proteins | |
| IgvfCatalogApi | coding_variants_summary | GET /coding-variants/phenotypes/score-summary | |
| IgvfCatalogApi | coding_variants_count_from_gene | GET /coding-variants/phenotypes-count | |
| IgvfCatalogApi | ontology_term_parents | GET /ontology-terms/{ontology_term_id}/parents | |
| IgvfCatalogApi | ontology_term_children | GET /ontology-terms/{ontology_term_id}/children | |
| IgvfCatalogApi | ontology_term_transitive_closure | GET /ontology-terms/{ontology_term_id_start}/transitive-closure/{ontology_term_id_end} | |
| IgvfCatalogApi | variants_from_variant_id | GET /variants/variant-ld | |
| IgvfCatalogApi | coding_variants_from_variants | GET /variants/coding-variants | |
| IgvfCatalogApi | drugs_from_variants | GET /variants/drugs | |
| IgvfCatalogApi | disease_from_variants | GET /variants/diseases | |
| IgvfCatalogApi | variants_from_coding_variants | GET /coding-variants/variants | |
| IgvfCatalogApi | transcripts_from_genes | GET /genes/transcripts | |
| IgvfCatalogApi | genes_transcripts_genes | GET /genes/transcripts/genes | |
| IgvfCatalogApi | proteins_from_genes | GET /genes/proteins | |
| IgvfCatalogApi | pathways_from_genes | GET /genes/pathways | |
| IgvfCatalogApi | genes_genes | GET /genes/genes | |
| IgvfCatalogApi | diseases_from_genes | GET /genes/diseases | |
| IgvfCatalogApi | genes_from_transcripts | GET /transcripts/genes | |
| IgvfCatalogApi | proteins_from_transcripts | GET /transcripts/proteins | |
| IgvfCatalogApi | transcripts_from_proteins | GET /proteins/transcripts | |
| IgvfCatalogApi | genes_from_proteins | GET /proteins/genes | |
| IgvfCatalogApi | complexes_from_proteins | GET /proteins/complexes | |
| IgvfCatalogApi | proteins_from_complexes | GET /complexes/proteins | |
| IgvfCatalogApi | motifs_from_proteins | GET /proteins/motifs | |
| IgvfCatalogApi | proteins_from_motifs | GET /motifs/proteins | |
| IgvfCatalogApi | genes_from_pathways | GET /pathways/genes | |
| IgvfCatalogApi | pathways_from_pathways | GET /pathways/pathways | |
| IgvfCatalogApi | annotations_from_go_terms | GET /go-terms/gene-products | |
| IgvfCatalogApi | go_terms_from_annotations | GET /gene-products/go-terms | |
| IgvfCatalogApi | variants_from_diseases | GET /diseases/variants | |
| IgvfCatalogApi | genes_from_diseases | GET /diseases/genes | |
| IgvfCatalogApi | variants_from_drugs | GET /drugs/variants | |
| IgvfCatalogApi | files_filesets | GET /files-filesets | |
| IgvfCatalogApi | llm_query | POST /llm-query |
Documentation For Models
- AccessibleGenomicElement
- AccessibleGenomicElementPromoterOf
- Annotations
- AnnotationsFromGoTerms
- Biosamples
- BiosamplesFromGenomicElements
- BiosamplesFromGenomicElementsBiosample
- BiosamplesFromGenomicElementsGenomicElement
- BiosamplesFromVariants
- BiosamplesFromVariantsGenomicElement
- BiosamplesFromVariantsVariant
- CaddScores
- CellTypes
- CellTypes2
- CodingVariant
- CodingVariants
- CodingVariantsFromGenes
- CodingVariantsFromPhenotypes
- CodingVariantsSummary
- Complex
- ComplexComplexAssembly
- ComplexesFromProteins
- ComplexesFromProteinsComplex
- ComplexesFromProteinsProtein
- DiseaseFromVariants
- DiseaseFromVariantsSequenceVariant
- DiseasesFromGenes
- DiseasesFromGenesGene
- Drug
- DrugsFromVariants
- DrugsFromVariantsDrug
- Elements
- EnhancerGenePredictions
- EnhancerGenePredictionsElements
- FilesFilesets
- Gene
- Gene4
- Gene6
- GeneCompact
- GeneNoSynonyms
- GeneRef
- Genes
- Genes2
- GenesFromGenomicElements
- GenesFromGenomicElementsGene
- GenesFromGenomicElementsGenomicElement
- GenesFromGenomicElementsPValue
- GenesFromPathways
- GenesFromPathwaysPathway
- GenesFromProteins
- GenesFromTranscripts
- GenesFromTranscriptsTranscript
- GenesFromVariants
- GenesFromVariantsSequenceVariant
- GenesFromVariantsStudy
- GenesGenes
- GenesGenesGene1
- GenesProteinsFromVariants
- GenesProteinsGenesProteins
- GenesStructure
- GenesTranscriptsGenes
- GenesTranscriptsGenesTranscript
- GenomicElement
- GenomicElement2
- GenomicElement4
- GenomicElement5
- GenomicElement7
- GenomicElement9
- GenomicElementFull
- GenomicElementsFromGenomicElements
- GenomicElementsFromGenomicElementsPerturbedGenomicElement
- GenomicElementsFromPhenotypes
- GenomicElementsFromPhenotypesPhenotype
- GenomicElementsFromVariants
- GenomicElementsPredictionsFromVariant
- Grn
- IdName
- InlineObject
- InlineObjectIssuesInner
- LinkedFeature
- LlmQuery
- LlmQueryRequest
- MethodCount
- MethodsAndContexts
- Motif
- MotifsFromProteins
- MotifsFromProteinsMotif
- NearestGene
- NearestGenes
- OntologyTerm
- OntologyTermBasic
- OntologyTermChildren
- OntologyTermTransitiveClosure
- Paths
- Pathway
- PathwaysFromPathways
- Phenotype
- PhenotypeRef
- PhenotypesFromVariants
- PhenotypesFromVariants37
- PhenotypesFromVariantsStudy
- PhenotypesFromVariantsVariant
- Predictions
- Predictions2
- PredictionsFromVariants
- Protein
- ProteinBasic
- ProteinChange
- ProteinCompact
- ProteinComplexOption
- ProteinsFromTranscripts
- ProteinsFromTranscriptsProtein
- ProteinsFromVariants
- ProteinsFromVariantsBiosampleTerm
- ProteinsFromVariantsProteinComplex
- ProteinsProteins
- ProteinsProteinsProtein1
- QtlSummaryEndpoint
- Qtls
- Qtls3
- Related
- RelatedGene
- RelatedItem
- RelatedSources
- Scores
- SequenceVariant
- SequenceVariant9
- Sources
- Sources4
- Study
- Study2
- StudyParameters
- Summary
- TargetGene
- TfBinding
- Transcript
- Variant
- VariantAnnotations
- VariantBasic
- VariantMinimal
- VariantRef
- VariantSummary
- Variants
- VariantsAllelesValue
- VariantsFromDrugs
- VariantsFromPhenotypesItem
- VariantsFromVariantID
- VariantsFromVariantIDSequenceVariant
- VariantsFromVariantIDSummary
- VariantsGenomicElementsGenes
- VariantsRegionSummary
Documentation For Authorization
Authentication schemes defined for the API:
Authorization
- Type: Bearer authentication
Author
1 maintainer
Metadata
1 maintainer
Release files for igvf-catalog-client 1.3.0
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