Module phc.easy.omics.options.genomic_short_variant

Classes

class NUM_DECIMAL_RANGE (...)

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

Ancestors

• pydantic.types.ConstrainedStr
• builtins.str

Class variables

var curtail_length

var max_length

var min_length

var regex

var strict

var strip_whitespace

var to_lower

var to_upper

class NUM_RANGE (...)

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

Ancestors

• pydantic.types.ConstrainedStr
• builtins.str

Class variables

var curtail_length

var max_length

var min_length

var regex

var strict

var strip_whitespace

var to_lower

var to_upper

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 if the input data cannot be parsed to form a valid model.

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_items=1)
    include: List[GenomicVariantInclude] = ["vcf"]
    gene: List[str] = []
    rs_id: List[constr(regex=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]

    @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
• pydantic.utils.Representation

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[ConstrainedStrValue]

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[ConstrainedStrValue]

var min_allele_frequency : Optional[ConstrainedStrValue]

var pop_allele_frequency : Optional[ConstrainedStrValue]

var position : List[Union[int, ConstrainedStrValue]]

var protein_changes : List[str]

var quality : List[str]

var read_depth : List[str]

var ref_read_depth : List[str]

var rs_id : List[ConstrainedStrValue]

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 dict(self)

Inherited from: PagingApiOptions.dict

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.