skbio.embedding.SequenceEmbedding

class skbio.embedding.SequenceEmbedding(embedding, sequence, **kwargs)

Embedding for a biological sequence.

Parameters:

embeddingarray_like

The embedding of the sequence. Row vectors correspond to the latent character coordinates.

sequencestr, Sequence, or 1D ndarray

Characters representing the sequence itself.

See also

Embedding

skbio.sequence.Sequence

Attributes

sequence

String representation of the underlying sequence.

Attributes (inherited)

embedding	The embedding tensor.
ids	IDs corresponding to each row of the embedding.

Methods (inherited)

bytes	Bytes representation of string encoding.
read	Create a new SequenceEmbedding instance from a file.
write	Write an instance of SequenceEmbedding to a file.

Special methods

__str__

String representation of the underlying sequence.

Special methods (inherited)

__eq__	Return self==value.
__ge__	Return self>=value.
__getstate__	Helper for pickle.
__gt__	Return self>value.
__hash__	Return hash(self).
__le__	Return self<=value.
__lt__	Return self<value.
__ne__	Return self!=value.

Details

sequence

String representation of the underlying sequence.

__str__()

String representation of the underlying sequence.