How to use the gnomad.resources.resource_utils.VersionedMatrixTableResource function in gnomad

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github macarthur-lab / gnomad_hail / gnomad / resources / grch38 / gnomad.py View on Github external
VersionedMatrixTableResource,
    MatrixTableResource,
    VersionedTableResource,
    DataException,
)
from typing import Optional

CURRENT_EXOME_RELEASE = ""
CURRENT_GENOME_RELEASE = "3.0"
EXOME_RELEASES = []
GENOME_RELEASES = ["3.0"]
DATA_TYPES = ["genomes"]

GENOME_POPS = ["AFR", "AMI", "AMR", "ASJ", "EAS", "FIN", "NFE", "SAS", "OTH"]

gnomad_syndip = VersionedMatrixTableResource(
    default_version="3.0",
    versions={
        "3.0": MatrixTableResource(
            path="gs://gnomad-public/truth-sets/hail-0.2/gnomad_v3_syndip.b38.mt"
        )
    },
)

na12878 = VersionedMatrixTableResource(
    default_version="3.0",
    versions={
        "3.0": MatrixTableResource(
            path="gs://gnomad-public/truth-sets/hail-0.2/gnomad_v3_na12878.mt"
        )
    },
)
github macarthur-lab / gnomad_hail / gnomad / resources / grch38 / gnomad.py View on Github external
EXOME_RELEASES = []
GENOME_RELEASES = ["3.0"]
DATA_TYPES = ["genomes"]

GENOME_POPS = ["AFR", "AMI", "AMR", "ASJ", "EAS", "FIN", "NFE", "SAS", "OTH"]

gnomad_syndip = VersionedMatrixTableResource(
    default_version="3.0",
    versions={
        "3.0": MatrixTableResource(
            path="gs://gnomad-public/truth-sets/hail-0.2/gnomad_v3_syndip.b38.mt"
        )
    },
)

na12878 = VersionedMatrixTableResource(
    default_version="3.0",
    versions={
        "3.0": MatrixTableResource(
            path="gs://gnomad-public/truth-sets/hail-0.2/gnomad_v3_na12878.mt"
        )
    },
)


def _public_release_ht_path(data_type: str, version: str) -> str:
    """
    Get public release table path

    :param data_type: One of "exomes" or "genomes"
    :param version: One of the release versions of gnomAD on GRCh38
    :return: Path to release Table
github macarthur-lab / gnomad_hail / gnomad / resources / grch37 / reference_data.py View on Github external
versions={
        "20181028": TableResource(
            path="gs://gnomad-public/resources/grch37/clinvar/clinvar_20181028.vep.ht",
            import_func=import_sites_vcf,
            import_args={
                "path": "gs://gnomad-public/resources/grch37/clinvar/clinvar_20181028.vcf.bgz",
                "force_bgz": True,
                "skip_invalid_loci": True,
                "min_partitions": 100,
                "reference_genome": "GRCh37",
            },
        )
    },
)

kgp_phase_3 = VersionedMatrixTableResource(
    default_version="phase_3_split",
    versions={
        "phase_3_split": MatrixTableResource(
            path="gs://gnomad-public/resources/grch37/kgp/1000Genomes_phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.split.mt",
            import_func=hl.import_vcf,
            import_args={
                "path": "gs://genomics-public-data/1000-genomes-phase-3/vcf-20150220/ALL.chr*.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf",
                "force_bgz": True,
                "skip_invalid_loci": True,
                "min_partitions": 300,
                "reference_genome": "GRCh37",
            },
        ),
        "phase_3": MatrixTableResource(
            path="gs://gnomad-public/resources/grch37/kgp/1000Genomes_phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.mt",
            import_func=hl.import_vcf,