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([format])	Create a new SequenceEmbedding instance from a file.
write(file[, format])	Write an instance of SequenceEmbedding to a file.

Special methods

__str__()

String representation of the underlying sequence.

Special methods (inherited)

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

Details

sequence

String representation of the underlying sequence.

__str__()

String representation of the underlying sequence.