pandas_genomics.scalars.Genotype

class pandas_genomics.scalars.Genotype(variant: pandas_genomics.scalars.Variant, allele_idxs: Optional[Union[Tuple[int], List[int]]] = None, score: Optional[int] = None)

Genotype information associated with a specific variant. Defaults to using an anonymous variant with two unknown alleles (diploid). Usually created with methods on ~Variant

Parameters

variant: pandas_genomics.scalars.variant.Variant

allele_idxs: List[int]

Alleles encoded as indexes into the variant allele list

score: int, optional

A quality score for the Genotype between 0 and 254. 255 or < 0 is treated as missing.

Examples

>>> variant = Variant('12', 112161652, 'rs12462')
>>> genotype = variant.make_genotype_from_str('C/T')
>>> print(genotype)
C/T

>>> missing_genotype = Genotype(variant)
>>> print(missing_genotype)
<Missing>

__init__(variant: pandas_genomics.scalars.Variant, allele_idxs: Optional[Union[Tuple[int], List[int]]] = None, score: Optional[int] = None)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(variant[, allele_idxs, score])	Initialize self.
is_missing()	Returns