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
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.

Built-ins

__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).

Methods

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