pandas_genomics.arrays.GenotypeDtype

class pandas_genomics.arrays.GenotypeDtype(variant: Optional[pandas_genomics.scalars.Variant] = None)[source]

An ExtensionDtype for genotype data.

Parameters
variant: Variant or None

The ~Variant associated with the genotype. If None, use an anonymous variant

Examples

v = Variant(chromosome=’12’, position=112161652, id=’rs12462’, ref=’T’, alt=[‘C’,], score=25) >>> GenotypeDtype(v) genotype(2n)[12; 112161652; rs12462; T; C]Q25

Attributes
variant: Variant

The variant that the datatype is specific to

__init__(variant: Optional[pandas_genomics.scalars.Variant] = None)[source]

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

Methods

__init__([variant])

Initialize self.

construct_array_type()

Return the array type associated with this dtype

construct_from_string(string)

Construct a GenotypeDtype from a string.

from_genotype(genotype)

Construct a GenotypeDtype from a Genotype.

is_dtype(dtype)

Return a boolean if the passed type can be processed as this dtype

reset_cache()

clear the cache

unpack_genotype(genotype)

Attributes

base

isbuiltin

isnative

itemsize

kind

na_value

Return the genotype with variant information but no alleles specified

name

A string identifying the data type.

names

Ordered list of field names, or None if there are no fields.

num

shape

subdtype