pandas_genomics.scalars.Variant

class pandas_genomics.scalars.Variant(chromosome: Optional[str] = None, position: int = 0, id: Optional[str] = None, ref: Optional[str] = 'N', alt: Optional[Union[List[str], str]] = None, ploidy: Optional[int] = None, score: Optional[int] = None)

Information about a variant.

Parameters

chromosome: str, optional

None by default, through this usually is not desired.

position: int, optional

(1-based, the default is 0 for none/unknown)

id: str, optional

None by default

ref: str, optional

Reference allele, ‘N’ by default

alt: List[str] or str, optional

One (or a list of) possible alternate alleles, empty list by default

ploidy: int, optional

The number of alleles that should be present. Assumed to be 2 if not specified.

score: int, optional

A quality score for the Variant. No assumptions are made about the meaning.

Notes

Missing alleles are shown as ., such as A/. or ./.

Examples

>>> variant = Variant('12', 112161652, id='rs12462', ref='A', alt=['C', 'T'])
>>> print(variant)
rs12462[chr=12;pos=112161652;ref=A;alt=C,T]

__init__(chromosome: Optional[str] = None, position: int = 0, id: Optional[str] = None, ref: Optional[str] = 'N', alt: Optional[Union[List[str], str]] = None, ploidy: Optional[int] = None, score: Optional[int] = None)

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

Methods

__init__([chromosome, position, id, ref, …])	Initialize self.
add_allele(allele)	Add a potential allele to the variant
as_dict()	Return the variant information as a dictionary
get_allele_from_idx(idx)	Get the allele corresponding to an index value for this variant
get_idx_from_allele(allele[, add])	Get the integer value for an allele based on this variant’s list of alleles, optionally adding it as a new allele
is_same_position(other)	Confirms this is a variant at the same position
is_valid_allele_idx(idx)	Validate the integer value for an allele with respect to this variant
make_genotype(*alleles[, add_alleles])	Create a Genotype object associated with this variant using the specified allele(s)
make_genotype_from_str(gt_str[, sep, …])	Create a Genotype object associated with this variant using the specified allele string

Attributes

alt
ref