skbio.embedding.ProteinVector

class skbio.embedding.ProteinVector(vector, sequence, **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

Default write format for this object: embed.

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 (inherited)

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

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.
__str__	Return str(self).

Details

default_write_format = 'embed'

Default write format for this object: embed.