skbio.alignment.AlignPath.from_bits

classmethod AlignPath.from_bits(bits, starts=None)

Create an alignment path from a bit array (0 - character, 1 - gap).

Parameters:

bitsarray_like of (0, 1) of shape (n_seqs, n_positions)

Array of zeros (character) and ones (gap) which represent the alignment.

startsarray_like of int of shape (n_sequences,), optional

Start position (0-based) of each sequence in the alignment. If omitted, will set as zeros.

Returns:

AlignPath

The alignment path created from the given bit array.

Examples

>>> import numpy as np
>>> from skbio.alignment import AlignPath
>>> bit_arr = np.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]])
>>> path = AlignPath.from_bits(bit_arr)
>>> path
AlignPath
Shape(sequence=3, position=8)
lengths: [2 2 2 1 1]
states: [0 2 0 6 0]