fountain-life-service-clients 3.30.0__tar.gz → 3.31.0__tar.gz

{fountain_life_service_clients-3.30.0 → fountain_life_service_clients-3.31.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fountain-life-service-clients
-Version: 3.30.0
+Version: 3.31.0
 Summary: 
 License: UNLICENSED
 Author: Fountain Life

fountain_life_service_clients-3.31.0/fountain_life_service_clients/genomics_service.py

@@ -0,0 +1,200 @@
+# This file was generated automatically. Do not edit it directly.
+from typing import (
+    List,
+    Literal,
+    NotRequired,
+    Optional,
+    TypedDict,
+    Union,
+    Unpack,
+    cast,
+)
+
+from fountain_life_service_clients._base_client import (
+    AlphaConfig,
+    AlphaResponse,
+    BaseClient,
+)
+
+SearchVariantsRequest = TypedDict(
+    "SearchVariantsRequest",
+    {
+        "variantSetIds": str,
+        "include": NotRequired[str],
+        "sequenceType": NotRequired[Union[Literal["somatic"], Literal["germline"]]],
+        "gene": NotRequired[Union[str, List[str]]],
+        "aminoAcidChange": NotRequired[Union[str, List[str]]],
+        "drugAssociations": NotRequired[bool],
+        "hasJaxKnowledge": NotRequired[bool],
+        "transcript_in_jaxckb": NotRequired[bool],
+        "cosmic_sample_count": NotRequired[float],
+        "class": NotRequired[Union[str, List[str]]],
+        "group": NotRequired[Union[str, List[str]]],
+        "impact": NotRequired[Union[str, List[str]]],
+        "biotype": NotRequired[Union[str, List[str]]],
+        "rs_id": NotRequired[Union[str, List[str]]],
+        "chromosome": NotRequired[Union[str, List[str]]],
+        "clinvar_allele_id": NotRequired[Union[str, List[str]]],
+        "clinvar_disease": NotRequired[Union[str, List[str]]],
+        "clinvar_review": NotRequired[Union[str, List[str]]],
+        "clinvar_significance": NotRequired[Union[str, List[str]]],
+        "clinvar_submission": NotRequired[Union[str, List[str]]],
+        "transcript_gene": NotRequired[Union[str, List[str]]],
+        "transcript_gene_id": NotRequired[Union[str, List[str]]],
+        "transcript_classification": NotRequired[Union[str, List[str]]],
+        "transcript_group": NotRequired[Union[str, List[str]]],
+        "transcript_impact": NotRequired[Union[str, List[str]]],
+        "transcript_id": NotRequired[Union[str, List[str]]],
+        "transcript_biotype": NotRequired[Union[str, List[str]]],
+        "transcript_exon_intron_rank": NotRequired[Union[str, List[str]]],
+        "transcript_hgvs_amino_acid_change": NotRequired[Union[str, List[str]]],
+        "transcript_nucleotide_change": NotRequired[Union[str, List[str]]],
+        "transcript_jax_protein_effect": NotRequired[Union[str, List[str]]],
+        "transcript_jax_knowledge": NotRequired[Union[str, List[str]]],
+        "cosmic_id": NotRequired[Union[str, List[str]]],
+        "cosmic_mutation_status": NotRequired[Union[str, List[str]]],
+        "cosmic_histology": NotRequired[Union[str, List[str]]],
+        "cosmic_tumor_site": NotRequired[Union[str, List[str]]],
+        "dbnsfp_fathmm_pred": NotRequired[Union[str, List[str]]],
+        "dbnsfp_mutationtaster_pred": NotRequired[Union[str, List[str]]],
+        "dbnsfp_sift_pred": NotRequired[Union[str, List[str]]],
+        "sample_zygosity": NotRequired[Union[str, List[str]]],
+        "sample_genotype": NotRequired[Union[str, List[str]]],
+        "sample_filter": NotRequired[Union[str, List[str]]],
+        "sample_vendsig": NotRequired[Union[str, List[str]]],
+        "sequence_type": NotRequired[Union[str, List[str]]],
+        "position": NotRequired[Union[str, List[str]]],
+        "clinvar_near_variant": NotRequired[Union[str, List[str]]],
+        "cosmic_near_variant": NotRequired[Union[str, List[str]]],
+        "minimum_allele_frequency": NotRequired[Union[str, List[str]]],
+        "maximum_allele_frequency": NotRequired[Union[str, List[str]]],
+        "population_allele_frequency": NotRequired[Union[str, List[str]]],
+        "exac_allele_frequency": NotRequired[Union[str, List[str]]],
+        "exac_homozygous": NotRequired[Union[str, List[str]]],
+        "dbnsfp_damaging_count": NotRequired[Union[str, List[str]]],
+        "dbnsfp_damaging_predictor": NotRequired[Union[str, List[str]]],
+        "dbnsfp_damaging_vote": NotRequired[Union[str, List[str]]],
+        "dbnsfp_fathmm_rankscore": NotRequired[Union[str, List[str]]],
+        "dbnsfp_mean_rankscore": NotRequired[Union[str, List[str]]],
+        "dbnsfp_mean_rankscore_predictor": NotRequired[Union[str, List[str]]],
+        "dbnsfp_mutationtaster_rankscore": NotRequired[Union[str, List[str]]],
+        "dbnsfp_sift_rankscore": NotRequired[Union[str, List[str]]],
+        "sample_allele_frequency": NotRequired[Union[str, List[str]]],
+        "sample_quality": NotRequired[Union[str, List[str]]],
+        "sample_read_depth": NotRequired[Union[str, List[str]]],
+        "sample_alternate_read_depth": NotRequired[Union[str, List[str]]],
+        "sample_reference_read_depth": NotRequired[Union[str, List[str]]],
+        "nextPageToken": NotRequired[str],
+        "pageSize": NotRequired[float],
+    },
+)
+
+
+class Clinvar(TypedDict):
+    nearVariant: float
+
+
+class Cosmic(TypedDict):
+    sampleCount: float
+    nearVariant: float
+    tumorSite: NotRequired[str]
+    histology: NotRequired[str]
+    cosmicId: NotRequired[str]
+    status: NotRequired[str]
+
+
+EnsemblCanonItem = TypedDict(
+    "EnsemblCanonItem",
+    {
+        "class": NotRequired[str],
+        "impact": NotRequired[str],
+        "gene": NotRequired[str],
+        "geneId": NotRequired[str],
+        "transcriptId": NotRequired[str],
+        "biotype": NotRequired[str],
+        "exonIntronRank": NotRequired[str],
+        "nucleotideChange": NotRequired[str],
+        "aminoAcidChange": NotRequired[str],
+        "hgvsAminoAcidChange": NotRequired[str],
+    },
+)
+
+
+class Dbnsfp(TypedDict):
+    siftPred: List[Optional[str]]
+    mutationTasterPred: List[Optional[str]]
+    fathmmPred: List[Optional[str]]
+
+
+EnsemblItem = TypedDict(
+    "EnsemblItem",
+    {
+        "class": NotRequired[str],
+        "impact": NotRequired[str],
+        "gene": NotRequired[str],
+        "geneId": NotRequired[str],
+        "transcriptId": NotRequired[str],
+        "biotype": NotRequired[str],
+        "exonIntronRank": NotRequired[str],
+        "nucleotideChange": NotRequired[str],
+        "aminoAcidChange": NotRequired[str],
+        "hgvsAminoAcidChange": NotRequired[str],
+    },
+)
+
+
+class Vcf(TypedDict):
+    quality: float
+    filter: str
+    variantAllelicFrequency: float
+    coverage: str
+
+
+class Item(TypedDict):
+    id: str
+    chromosome: str
+    reference: str
+    alternate: str
+    position: float
+    minimumAlleleFrequency: float
+    maximumAlleleFrequency: float
+    gnomadAlleleFrequency: float
+    gnomadHomozygous: float
+    rsid: str
+    zygosity: str
+    clinvar: Clinvar
+    cosmic: Cosmic
+    ensemblCanon: List[EnsemblCanonItem]
+    dbnsfp: Dbnsfp
+    ensembl: NotRequired[List[EnsemblItem]]
+    vcf: NotRequired[Vcf]
+
+
+class Links(TypedDict):
+    self: str
+    next: NotRequired[str]
+
+
+class Invalid(TypedDict):
+    variantSetIds: List[str]
+
+
+class SearchVariantsResponse(TypedDict):
+    items: NotRequired[List[Item]]
+    links: Links
+    sorted: NotRequired[bool]
+    count: NotRequired[float]
+    invalid: NotRequired[Invalid]
+
+
+class GenomicsServiceClient(BaseClient):
+    def __init__(self, **cfg: Unpack[AlphaConfig]):
+        kwargs = {"target": "lambda://genomics-service:deployed", **(cfg or {})}
+        super().__init__(**kwargs)
+
+    async def search_variants(self, body: SearchVariantsRequest):
+        """Search for variants"""
+        res = await self.client.request(
+            path="/v1/genomics/variants/_search", method="POST", body=cast(dict, body)
+        )
+        return cast(AlphaResponse[SearchVariantsResponse], res)

{fountain_life_service_clients-3.30.0 → fountain_life_service_clients-3.31.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fountain-life-service-clients"
-version = "3.30.0"
+version = "3.31.0"
 description = ""
 authors = ["Fountain Life <dev@fountainlife.com>"]
 license = "UNLICENSED"