Cloud API

life sciences
genomics (vcf)
reference

read_allele_frequency

Description

Read variant status

Usage

tiledb.cloud.vcf.read_allele_frequency(dataset_uri, region)

Parameters

  • dataset_uri: dataset URI
  • region: genomics region to read

calc_af

Description

Consolidate allele count (AC) and compute allele number (AN), allele frequency (AF)

Usage

tiledb.cloud.vcf.allele_frequency.calc_af(df)

Parameters

  • df: a pandas dataframe

ingest

Usage

tiledb.cloud.vcf.ingest(dataset_uri, acn = None, config = None, namespace = None, register_name = None, search_uri = None, pattern = None, ignore = None, sample_list_uri = None, metadata_uri = None, metadata_attr = "uri", max_files = None, contigs = Contigs.ALL, resume = True, extra_attrs = repr(DEFAULT_ATTRIBUTES), vcf_attrs = None, anchor_gap = None, compression_level = None, manifest_batch_size = MANIFEST_BATCH_SIZE, manifest_workers = MANIFEST_WORKERS, vcf_batch_size = VCF_BATCH_SIZE, vcf_workers = VCF_WORKERS, ingest_resources = None, verbose = False, create_index = True, trace_id = None, consolidate_stats = True, aws_find_mode = False)

Description

Ingest samples into a dataset.

Parameters

  • dataset_uri: dataset URI
  • acn: Access Credentials Name (ACN) registered in TileDB Cloud (ARN type), defaults to None
  • config: config dictionary, defaults to None
  • namespace: TileDB-Cloud namespace, defaults to None
  • register_name: name to register the dataset with on TileDB Cloud, defaults to None
  • search_uri: URI to search for VCF files, defaults to None
  • pattern: Unix shell style pattern to match when searching for VCF files, defaults to None
  • ignore: Unix shell style pattern to ignore when searching for VCF files, defaults to None
  • sample_list_uri: URI with a list of VCF URIs, defaults to None
  • metadata_uri: URI of metadata array holding VCF URIs, defaults to None
  • metadata_attr: name of metadata attribute containing URIs, defaults to uri
  • max_files: maximum number of VCF URIs to read/find, defaults to None (no limit)
  • max_samples: maximum number of samples to ingest, defaults to None (no limit)
  • contigs: contig mode (Contigs.ALL | Contigs.CHROMOSOMES | Contigs.OTHER | Contigs.ALL_DISABLE_MERGE) or list of contigs to ingest, defaults to Contigs.ALL
  • resume: enable resume ingestion mode, defaults to True
  • extra_attrs: INFO/FORMAT fields to materialize, defaults to repr(DEFAULT_ATTRIBUTES)
  • vcf_attrs: VCF with all INFO/FORMAT fields to materialize, defaults to None
  • anchor_gap: anchor gap for VCF dataset, defaults to None
  • compression_level: zstd compression level for the VCF dataset, defaults to None (uses the default level in TileDB-VCF)
  • manifest_batch_size: batch size for manifest ingestion, defaults to MANIFEST_BATCH_SIZE
  • manifest_workers: number of workers for manifest ingestion, defaults to MANIFEST_WORKERS
  • vcf_batch_size: batch size for VCF ingestion, defaults to VCF_BATCH_SIZE
  • vcf_workers: number of workers for VCF ingestion, defaults to VCF_WORKERS
  • vcf_threads: number of threads for VCF ingestion, defaults to VCF_THREADS
  • ingest_resources: manual override for ingest UDF resources, defaults to None
  • verbose: verbose logging, defaults to False
  • create_index: force creation of a local index file, defaults to True
  • trace_id: trace ID for logging, defaults to None
  • consolidate_stats: consolidate the stats arrays, defaults to True
  • aws_find_mode: use AWS CLI to find VCFs, defaults to False

ingest_annotations

Usage

tiledb.cloud.vcf.ingest_annotations(dataset_uri, vcf_uri = None, search_uri = None, pattern = None, ignore = None, create_index = True, config = None, acn = None, namespace = None, register_name = None, ingest_resources = None, verbose = False)

Description

Ingest annotation VCF into a dataset. For example, a ClinVar or gnomAD VCF.

Parameters

  • dataset_uri: dataset URI
  • vcf_uri: VCF URI, defaults to None
  • search_uri: URI to search for VCF files, defaults to None
  • pattern: Unix shell style pattern to match when searching for VCF files, defaults to None
  • ignore: Unix shell style pattern to ignore when searching for VCF files, defaults to None
  • create_index: force creation of a local index file, defaults to True
  • config: config dictionary, defaults to None
  • acn: Access Credentials Name (ACN) registered in TileDB Cloud (ARN type), defaults to None
  • namespace: TileDB-Cloud namespace, defaults to None
  • register_name: name to register the dataset with on TileDB Cloud, defaults to None
  • ingest_resources: manual override for ingest UDF resources, defaults to None
  • verbose: verbose logging, defaults to False

build_read_dag

Usage

tiledb.cloud.vcf.build_read_dag(dataset_uri, config = None, attrs = None, regions = None, bed_file = None, num_region_partitions = 1, samples = None, memory_budget_mb = 1024, af_filter = None, transform_result = None, max_sample_batch_size = 500, log_uri = None, namespace = None, resource_class = None, verbose = False)

Description

Build the DAG for a distributed read on a TileDB-VCF dataset.

Parameters

  • dataset_uri: dataset URI
  • config: config dictionary, defaults to None
  • attrs: attribute names to read, defaults to None
  • regions: genomics regions to read, defaults to None
  • bed_file: URI of a BED file containing genomics regions to read, defaults to None
  • num_region_partitions: number of region partitions, defaults to 1
  • samples: sample names to read, defaults to None
  • memory_budget_mb: VCF memory budget in MiB, defaults to 1024
  • af_filter: allele frequency filter, defaults to None
  • transform_result: function to apply to each partition; by default, does not transform the result
  • max_sample_batch_size: maximum number of samples to read in a single node, defaults to 500
  • log_uri: log array URI for profiling, defaults to None
  • namespace: TileDB-Cloud namespace, defaults to None
  • resource_class: TileDB-Cloud resource class for UDFs, defaults to None
  • verbose: verbose logging, defaults to False

Return values

DAG and result Node

read

Usage

tiledb.cloud.vcf.read(dataset_uri, config = None, attrs = None, regions = None, bed_file = None, num_region_partitions = 1, samples = None, memory_budget_mb = 1024, af_filter = None, transform_result = None, max_sample_batch_size = 500, log_uri = None, namespace = None, resource_class = None, verbose = False)

Description

Run a distributed read on a TileDB-VCF dataset.

Parameters

  • dataset_uri: dataset URI
  • config: config dictionary, defaults to None
  • attrs: attribute names to read, defaults to None
  • regions: genomics regions to read, defaults to None
  • bed_file: URI of a BED file containing genomics regions to read, defaults to None
  • num_region_partitions: number of region partitions, defaults to 1
  • samples: sample names to read, defaults to None
  • memory_budget_mb: VCF memory budget in MiB, defaults to 1024
  • af_filter: allele frequency filter, defaults to None
  • transform_result: function to apply to each partition; by default, does not transform the result
  • max_sample_batch_size: maximum number of samples to read in a single node, defaults to 500
  • log_uri: log array URI for profiling, defaults to None
  • namespace: TileDB-Cloud namespace, defaults to None
  • resource_class: TileDB-Cloud resource class for UDFs, defaults to None
  • verbose: verbose logging, defaults to False

Return value

  • Arrow table containing the query results