variantgrid_api

Python API client for VariantGrid Open source Variant database and analysis platform

See changelog

Install

python3 -m pip install variantgrid_api

Example

from variantgrid_api.api_client import VariantGridAPI
from variantgrid_api.data_models import EnrichmentKit

api = VariantGridAPI(server="https://variantgrid.com", api_token="YOUR_API_TOKEN")
enrichment_kit = EnrichmentKit(name="idt_haem", version=1)
result = api.create_enrichment_kit(enrichment_kit)

Annotate a VCF and download it back

Upload a VCF, have VariantGrid import + annotate any novel variants, then download the cohort-level annotated export (all samples, single-sample VCFs included). Annotation can take a while, so the quickest way in is the vg_api command line tool: the first call uploads, and running the same command again downloads the result once it's ready.

$ export VARIANTGRID_API_TOKEN=YOUR_API_TOKEN
$ vg_api annotate_vcf input.vcf.gz -o results/
Uploaded input.vcf.gz (id=13256).
Annotating input.vcf.gz - run the same command again later to download.

$ vg_api annotate_vcf input.vcf.gz -o results/        # once it's done
Annotated vcf written to results/input.vcf_annotated_v254_GRCh38.vcf.gz

From Python it's upload_file() / poll_upload_status() / download_annotated(), or the blocking annotate_vcf() one-liner. See Annotate a VCF on the wiki for batches, the submit-now/download-later pattern, and all the options.

Patients, specimens and extractions

VariantGrid can record which patient, specimen and extraction a lab's sequencing came from, and specimen-level measures such as TMB, MSI and GIS. This needs a server at or after SACGF/variantgrid#1716.

from variantgrid_api.data_models import Patient, Specimen, Extraction, ExternalReference, NucleicAcid

api.create_patient(Patient(patient_code="C0000001"))
api.create_specimen(Specimen(patient="C0000001", reference_id="2600000001"))
api.create_extraction(Extraction(specimen="2600000001", reference_id="2600000001C",
                                 nucleic_acid_source=NucleicAcid.DNA))
api.upload_file("sample.vcf.gz", path=None,
                metadata={"extraction": "2600000001C", "genome_build": "GRCh37"})

A bare string names a record by its local reference. Use ExternalReference(code=..., external_type=...) to name it by a LIMS identifier instead. See examples/example_tso500.py for a full run.

Talking to more than one VariantGrid version

Servers of different ages accept different calls. The client asks the server which features it has (GET api/v1/capabilities, fetched once on first use), and each call that needs a newer server checks that list first: the patient / specimen / extraction calls, specimen measures, link_sequencing_sample_extraction, the annotate flow (poll_upload_status, wait_for_annotation, download_annotated, annotate_vcf), and upload_file with metadata or file_type. A server without the capabilities endpoint counts as legacy and reports no features.

By default an unsupported call raises UnsupportedFeatureError. To run the same code against old and new servers, skip those calls instead: they log a warning and return None. upload_file is the exception: on a server without upload metadata it drops the metadata and still uploads the file.

from variantgrid_api.api_client import VariantGridAPI, UnsupportedFeaturePolicy

api = VariantGridAPI(server, api_token, unsupported_feature_policy=UnsupportedFeaturePolicy.SKIP)
api.create_patient(patient)        # skipped on a server without patients

# Uploads only when the server has an importer for this file type
api.upload_file("sample_CombinedVariantOutput.tsv", path=None,
                file_type="dragen_tso500_combined_variant_output")

Where the fallback isn't simply "do nothing", branch on api.supports("feature") or api.accepts_upload("file_type"). api.capabilities.version is useful for logging which server you reached. For tests, MockVariantGridAPI(capabilities=ServerCapabilities.LEGACY) behaves like an old server.

Testing

# Install required testing packages
python3 -m pip install -e ".[test]"
python3 -m pytest --cov=variantgrid_api