skbio.alignment.PairAlignPath.from_cigar

classmethod PairAlignPath.from_cigar(cigar, starts=None)

Create a pairwise alignment path from a CIGAR string.

Parameters:

cigarstr or bytes

CIGAR format string used to build the PairAlignPath.

startsarray_like of (int, int), optional

Start position of each sequence in the alignment. If omitted, will set as zeros.

Returns:

PairAlignPath

The pairwise alignment path created from the given CIGAR string.

Raises:

ValueError

CIGAR string is empty.

ValueError

CIGAR string contains invalid characters.

Examples

>>> from skbio.alignment import PairAlignPath
>>> cigar = "2M5P3D1I"
>>> path = PairAlignPath.from_cigar(cigar)
>>> path
<PairAlignPath, positions: 11, segments: 4, CIGAR: '2M5P3D1I'>