skbio.embedding.ProteinVector

class skbio.embedding.ProteinVector(vector, sequence: str, **kwargs)

Vector representation for a protein sequence.

Parameters:

vector1D or 2D array_like

The vector representation of the protein sequence. Typically a 1D array. Can also be a 2D array with only one row.

sequencestr, Sequence, or 1D ndarray

Characters representing the protein sequence itself.

See also

SequenceVector

skbio.sequence.Protein

Examples

>>> from skbio.embedding import ProteinVector
>>> import numpy as np
>>> vector = np.random.rand(10)
>>> sequence = "ACDEFGHIKL"
>>> ProteinVector(vector, sequence)
ProteinVector
--------------------------
Stats:
    length: 10
    vector dimension: 10
    has gaps: False
    has degenerates: False
    has definites: True
    has stops: False
--------------------------
0 ACDEFGHIKL

Attributes

default_write_format

Attributes (inherited)

embedding	The embedding tensor.
ids	IDs corresponding to each row of the embedding.
sequence	String representation of the underlying sequence.
vector	Vector representation for the biological entity.

Methods

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

Methods (inherited)

bytes()

Bytes representation of string encoding.

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.
__str__()	Return str(self).

Details

default_write_format = 'embed'