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igvf-catalog-client

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.

This Python package is automatically generated by the OpenAPI Generator project:

  • API version: 1.2.0
  • Package version: 1.2.0
  • Generator version: 7.14.0
  • Build package: org.openapitools.codegen.languages.PythonClientCodegen

Requirements.

Python 3.9+

Installation & Usage

pip install

If the python package is hosted on a repository, you can install directly using:

pip install git+https://github.com/IGVF-DACC/igvf-catalog-python-client.git

(you may need to run pip with root permission: sudo pip install git+https://github.com/IGVF-DACC/igvf-catalog-python-client.git)

Then import the package:

import igvf_catalog_client

Setuptools

Install via Setuptools.

python setup.py install --user

(or sudo python setup.py install to install the package for all users)

Then import the package:

import igvf_catalog_client

Tests

Execute pytest to run the tests.

Getting Started

Please follow the installation procedure and then run the following:

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 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 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

Documentation For Authorization

Authentication schemes defined for the API:

Authorization

  • Type: Bearer authentication

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Python API client for igvf catalog

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