pandas_genomics.arrays.GenotypeDtype

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

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)

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