Module phc.easy.omics.options.genomic_short_variant

Classes

class GenomicShortVariantOptions (**data: Any)

Options to pass to /v1/genomics/variants

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Expand source code

class GenomicShortVariantOptions(PagingApiOptions):
    """Options to pass to `/v1/genomics/variants`"""

    # TODO: Add remaining options from Omics Explorer in PHC
    # - Variant Quality
    # - Variant Allele Freq
    # - Combined In Silico Prediction
    # - Individual In Silico Predictors

    variant_set_ids: List[str] = Field(..., min_length=1)
    include: List[GenomicVariantInclude] = ["vcf"]
    gene: List[str] = []
    rs_id: List[constr(pattern=RS_ID)] = []
    chromosome: List[Chromosome] = []
    clinvar_allele_id: List[str] = []
    clinvar_disease: List[str] = []
    clinvar_review: List[ClinVarReview] = []
    clinvar_significance: List[ClinVarSignificance] = []
    cosmic_id: List[str] = []
    cosmic_status: List[str] = []
    cosmic_histology: List[str] = []
    cosmic_tumor_site: List[str] = []
    variant_class: List[str] = []  # Renamed from 'class'
    coding_effect: List[CodingEffect] = []
    impact: List[str] = []
    transcript_id: List[str] = []
    gene_class: List[GeneClass] = []
    protein_changes: List[str] = []
    sequence_type: List[str] = []
    position: List[Union[int, NUM_RANGE]] = []
    cosmic_min_count: Optional[int] = None
    min_allele_frequency: Optional[NUM_DECIMAL_RANGE] = None
    max_allele_frequency: Optional[NUM_DECIMAL_RANGE] = None
    pop_allele_frequency: Optional[NUM_DECIMAL_RANGE] = None
    exac_allele_frequency: Optional[NUM_DECIMAL_RANGE] = None
    exac_homozygous: List[str] = []
    dbnsfp_damaging_count: List[str] = []
    dbnsfp_damaging_predictor: List[str] = []
    dbnsfp_damaging_vote: List[str] = []
    dbnsfp_fathmm_rankscore: List[str] = []
    dbnsfp_fathmm_pred: List[str] = []
    dbnsfp_mean_rankscore: List[str] = []
    dbnsfp_mean_rankscore_predictor: List[str] = []
    dbnsfp_mutationtaster_rankscore: List[str] = []
    dbnsfp_mutationtaster_pred: List[str] = []
    dbnsfp_sift_rankscore: List[str] = []
    dbnsfp_sift_pred: List[str] = []
    zygosity: List[Zygosity] = []
    genotype: List[str] = []
    variant_allele_frequency: List[str] = []
    quality: List[str] = []
    read_depth: List[str] = []
    alt_read_depth: List[str] = []
    ref_read_depth: List[str] = []
    variant_filter: List[str] = []
    in_ckb: Optional[bool] = None

    @staticmethod
    def transform(key, value):
        if isinstance(value, list):
            value = ",".join(
                [elem if isinstance(elem, str) else str(elem) for elem in value]
            )
        elif isinstance(value, bool):
            value = "true" if value else None

        if key == "cosmic_min_count" and value is not None:
            return ("cosmicSampleCount", f"{value}:gte")

        return (MAPPINGS.get(key, key), value)

Ancestors

• PagingApiOptions
• pydantic.main.BaseModel

Class variables

var alt_read_depth : List[str]

var chromosome : List[Chromosome]

var clinvar_allele_id : List[str]

var clinvar_disease : List[str]

var clinvar_review : List[ClinVarReview]

var clinvar_significance : List[ClinVarSignificance]

var coding_effect : List[CodingEffect]

var cosmic_histology : List[str]

var cosmic_id : List[str]

var cosmic_min_count : Optional[int]

var cosmic_status : List[str]

var cosmic_tumor_site : List[str]

var dbnsfp_damaging_count : List[str]

var dbnsfp_damaging_predictor : List[str]

var dbnsfp_damaging_vote : List[str]

var dbnsfp_fathmm_pred : List[str]

var dbnsfp_fathmm_rankscore : List[str]

var dbnsfp_mean_rankscore : List[str]

var dbnsfp_mean_rankscore_predictor : List[str]

var dbnsfp_mutationtaster_pred : List[str]

var dbnsfp_mutationtaster_rankscore : List[str]

var dbnsfp_sift_pred : List[str]

var dbnsfp_sift_rankscore : List[str]

var exac_allele_frequency : Optional[str]

var exac_homozygous : List[str]

var gene : List[str]

var gene_class : List[GeneClass]

var genotype : List[str]

var impact : List[str]

var in_ckb : Optional[bool]

var include : List[GenomicVariantInclude]

var max_allele_frequency : Optional[str]

var min_allele_frequency : Optional[str]

var model_config

var pop_allele_frequency : Optional[str]

var position : List[Union[str, int]]

var protein_changes : List[str]

var quality : List[str]

var read_depth : List[str]

var ref_read_depth : List[str]

var rs_id : List[str]

var sequence_type : List[str]

var transcript_id : List[str]

var variant_allele_frequency : List[str]

var variant_class : List[str]

var variant_filter : List[str]

var variant_set_ids : List[str]

var zygosity : List[Zygosity]

Static methods

def transform(key, value)

Expand source code

@staticmethod
def transform(key, value):
    if isinstance(value, list):
        value = ",".join(
            [elem if isinstance(elem, str) else str(elem) for elem in value]
        )
    elif isinstance(value, bool):
        value = "true" if value else None

    if key == "cosmic_min_count" and value is not None:
        return ("cosmicSampleCount", f"{value}:gte")

    return (MAPPINGS.get(key, key), value)

Methods

def model_dump(self)

Inherited from: PagingApiOptions.model_dump

Usage docs: https://docs.pydantic.dev/2.10/concepts/serialization/#modelmodel_dump …