skbio.alignment.AlignPath.to_bits#

AlignPath.to_bits(expand=True)[source]#

Unpack the alignment path into an array of bits.

Changed in version 0.6.4: The default behavior now returns positions.

Parameters:

expandbool, optional: If True (default), each column in the returned array represents a position in the original alignment. If False, each column represents a segment in the alignment path.

Added in version 0.6.4.

Returns:

ndarray of (0, 1) of shape (n_sequences, n_positions or n_segments): Array of zeros (character) and ones (gap) which represent the alignment.

Examples

>>> from skbio import DNA, TabularMSA
>>> from skbio.alignment import AlignPath
>>> seqs = [
...    DNA('CGTCGTGC'),
...    DNA('CA--GT-C'),
...    DNA('CGTCGT-T')
... ]
>>> msa = TabularMSA(seqs)
>>> path = AlignPath.from_tabular(msa)

Return a bit array representing positions:

>>> path.to_bits()
array([[0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 1, 1, 0, 0, 1, 0],
       [0, 0, 0, 0, 0, 0, 1, 0]], dtype=uint8)

Return a bit array representing segments:

>>> path.to_bits(expand=False)
array([[0, 0, 0, 0, 0],
       [0, 1, 0, 1, 0],
       [0, 0, 0, 1, 0]], dtype=uint8)