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)[source]¶ 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)[source]¶ Initialize self. See help(type(self)) for accurate signature.
Methods
__init__
(variant[, allele_idxs, score])Initialize self.
is_missing
()- Returns