TabularMSA.
gap_frequencies
(axis='sequence', relative=False)[source]¶Compute frequency of gap characters across an axis.
State: Experimental as of 0.4.1.
Parameters: |
|
---|---|
Returns: | Vector of gap character frequencies across the specified axis. Will
have |
Return type: | 1D np.ndarray (int or float) |
Raises: |
|
Notes
If there are no positions in the MSA, axis='position'
, and
relative=True
, the relative frequency of gap characters in each
sequence will be np.nan
.
Examples
Compute frequency of gap characters for each position in the MSA (i.e., across the sequence axis):
>>> from skbio import DNA, TabularMSA
>>> msa = TabularMSA([DNA('ACG'),
... DNA('A--'),
... DNA('AC.'),
... DNA('AG.')])
>>> msa.gap_frequencies()
array([0, 1, 3])
Compute relative frequencies across the same axis:
>>> msa.gap_frequencies(relative=True)
array([ 0. , 0.25, 0.75])
Compute frequency of gap characters for each sequence (i.e., across the position axis):
>>> msa.gap_frequencies(axis='position')
array([0, 2, 1, 1])