alphagenome.data.genome.Variant

class alphagenome.data.genome.Variant(chromosome, position, reference_bases, alternate_bases, name='', info=<factory>)

Represents a genomic variant/mutation.

Differs from the Variant definition in a VCF file, which allows for multiple alternative bases and contains sample information. This Variant class does not include sample information or variant call quality information.

chromosome

The chromosome name (e.g., ‘chr1’, ‘1’).

position

The 1-based position of the variant on the chromosome.

reference_bases

The reference base(s) at the variant position. Most frequently (not always!), these correspond to the sequence in the reference genome at positions: [position, …, position + len(reference_bases) - 1]

alternate_bases

The alternate base(s) that replace the reference. For example, if sequence=’ACT’, position=2, reference_bases=’C’, alternate_bases=’TG’, then the actual (alternate) sequence would be ATGT.

name

An optional name for the variant (e.g., a dbSNP ID like rs206437).

info

An optional dictionary for additional variant information.

Attributes

Table

end	Returns the 0-based end position of the variant.
name
reference_interval	Returns an Interval for the variant's reference sequence.
start	Returns the 0-based start position of the variant.
chromosome
position
reference_bases
alternate_bases
info

Variant.end

Returns the 0-based end position of the variant.

Variant.name: str = ''

Variant.reference_interval

Returns an Interval for the variant’s reference sequence.

Variant.start

Returns the 0-based start position of the variant.

Variant.chromosome: str

Variant.position: int

Variant.reference_bases: str

Variant.alternate_bases: str

Variant.info: dict[str, Any]

Methods

Table

alternate_overlaps(interval)	Checks if the variant's alternate overlaps with the interval.
as_truncated_str([max_length])	Truncates the variant str's ref and alt bases to the given max length.
copy()	Returns a deep copy of the variant.
from_dict(dictionary)	Creates a Variant from a dictionary.
from_proto(variant)	Creates a Variant from a protobuf message.
from_str(string[, variant_format])	Creates a Variant from a string representation.
reference_overlaps(interval)	Checks if the variant's reference overlaps with the interval.
split(anchor)	Splits the variant into two at the anchor point.
to_dict()	Converts the variant to a dictionary.
to_proto()	Converts the variant to a protobuf message.

Variant.alternate_overlaps(interval)

Checks if the variant’s alternate overlaps with the interval.

Return type:

bool

Variant.as_truncated_str(max_length=50)

Truncates the variant str’s ref and alt bases to the given max length.

Variant.copy()

Returns a deep copy of the variant.

Return type:

Self

classmethod Variant.from_dict(dictionary)

Creates a Variant from a dictionary.

Return type:

Self

classmethod Variant.from_proto(variant)

Creates a Variant from a protobuf message.

Return type:

Self

classmethod Variant.from_str(string, variant_format=VariantFormat.DEFAULT)

Creates a Variant from a string representation.

Parameters:

• string (str) – The string representation.

• variant_format (VariantFormat (default: <VariantFormat.DEFAULT: 'default'>)) – The format of the variant string. By default, this uses “chromosome:position:ref>alt” (for example, “chr1:1024:A>C”). See VariantFormat for alternate formatting options.

Return type:

Self

Returns:

A Variant object.

Variant.reference_overlaps(interval)

Checks if the variant’s reference overlaps with the interval.

Return type:

bool

Variant.split(anchor)

Splits the variant into two at the anchor point.

If the anchor point falls within the variant’s reference sequence, the variant is split into two new variants: one upstream of the anchor and one downstream. If the anchor is outside the variant’s reference sequence, the original variant is returned on the appropriate side, and None on the other.

Example

position= 3 ref: …[ A C ]… alt: …..T G T C anchor=3 | returns: (chr1:3:A>T, chr1:4:C>GTC)

Parameters:

anchor (int) – The 0-based anchor point to split the variant.

Return type:

tuple[Optional[Self], Optional[Self]]

Returns:

A tuple of the upstream and downstream variants. If the variant is only on one side of the anchorpoint, then None is returned.

Variant.to_dict()

Converts the variant to a dictionary.

Return type:

dict[str, Any]

Variant.to_proto()

Converts the variant to a protobuf message.

Return type:

Variant