anyvar.vcf.ingest

Support processing and manipulation of VCF objects.

exception anyvar.vcf.ingest.RequiredAnnotationsError[source]: Raise when encountering incomplete or invalid VRS annotations

class anyvar.vcf.ingest.VcfRegistrar(data_proxy, **kwargs)[source]

Custom implementation of annotator class from VRS-Python. Rewrite some methods and values in order to enable use of existing AnyVar translator.

__init__(data_proxy, **kwargs)[source]

Initialize the VCFAnnotator class.

Parameters:: data_proxy (_DataProxy) – GA4GH sequence dataproxy instance.

annotate(input_vcf_path, output_vcf_path=None, vrs_attributes=False, assembly='GRCh38', compute_for_ref=True, require_validation=True, **kwargs)[source]

Calls the parent ‘annotate’ function, then adds the final batch of VRS objects to the database

Return type:: None

on_vrs_object(vcf_coords, vrs_allele, **kwargs)[source]

Adds the VRS object to the batcher, which handles bulk registration

Return type:: Allele | None

on_vrs_object_collection(vrs_alleles_collection, **kwargs)[source]

Perform clean-up operations (eg file writing) on VRS objects collected during VCF ingestion.

Parameters:: vrs_alleles_collection (list[Allele] | None) – VRS alleles constructed from ingested VCF
Return type:: None

raise_for_output_args(output_vcf_path, **kwargs)[source]

Raise an exception if no output (VCF, PKL, NDJSON) appears to be configured or declared.

Parameters:

output_vcf_path (Path | None) – VCF output path arg passed to annotate()
output_pkl_path – optional path to PKL output
output_ndjson_path – optional path to NDJSON output

Raises:

VCFAnnotatorArgsError – if no output args are given

Return type:

None

vrs_object_registration_batcher: VrsObjectRegistrationBatcher[source]

class anyvar.vcf.ingest.VrsObjectRegistrationBatcher(anyvar_instance)[source]

Handles bulk registration of a large number of VrsObjects in batches

BATCH_SIZE = 10000[source]

__init__(anyvar_instance)[source]

Initialize batch collection list and AnyVar instance to use for registration

Parameters:: anyvar_instance (AnyVar) – The AnyVar instance to use for registration
Returns:: None

add_to_batch(vrs_object)[source]

Adds a VRS Object to the current batch. If batch size limit is now met, register the whole batch.

Parameters:: vrs_object (Allele | SequenceLocation | SequenceReference) – The VrsObject to add to the batch
Return type:: None
Returns:: None

anyvar_instance: AnyVar[source]

batch_collection: list[Allele | SequenceLocation | SequenceReference][source]

register_batch()[source]

Registers a batch of vrs objects and resets the collection list to prepare for the next batch

Return type:: None

anyvar.vcf.ingest.register_existing_annotations(av, file_path, assembly, require_validation=False)[source]

Extract VRS allele parameters from a previously-annotated VCF and register them.

Parameters:

av (AnyVar) – AnyVar instance
file_path (Path) – path to VCF
assembly (str) – assembly used during VCF writing and annotation. Probably one of {"GRCh37", "GRCh38"}
require_validation (bool) – whether to check that annotated ID is correct

Return type:

Path | None

Returns:

Path to ID conflict file, if requested, or None otherwise

Raise:

ValueError if input VCF lacks required annotations