skbio.alignment.PairAlignPath

class skbio.alignment.PairAlignPath(lengths, states, starts=(0, 0))

Store a pairwise alignment path between two sequences.

PairAlignPath is a subclass of AlignPath, with additional methods specific to pairwise alignments, such as the processing of CIGAR strings.

Parameters:

lengthsarray_like of int of shape (n_segments,)

Length of each segment in the alignment.

statesarray_like of uint8 of shape (n_segments,)

Bits representing character (0) or gap (1) status per sequence per segment in the alignment.

startsarray_like of (int, int), optional

Start position (0-based) of each sequence in the alignment. Default is (0, 0).

See also

AlignPath

skbio.sequence.Sequence

skbio.alignment.TabularMSA

Attributes (inherited)

lengths	Array of lengths of segments in alignment path.
shape	Number of sequences (rows) and positions (columns).
starts	Array of start positions of sequences in the alignment.
states	Array of gap status of segments in alignment path.

Methods

from_bits(bits[, starts])	Create a pairwise alignment path from a bit array.
from_cigar(cigar[, starts])	Create a pairwise alignment path from a CIGAR string.
to_cigar([seqs])	Generate a CIGAR string representing the pairwise alignment path.

Methods (inherited)

from_coordinates(coords)	Create an alignment path from an array of segment coordinates.
from_indices(indices[, gap])	Create an alignment path from character indices in the original sequences.
from_tabular(msa)	Create an alignment path from a TabularMSA object.
stops()	Calculate the stop positions of sequences in the alignment.
to_bits([expand])	Unpack the alignment path into an array of bits.
to_coordinates()	Generate an array of segment coordinates in the original sequences.
to_indices([gap])	Generate an array of indices of characters in the original sequences.

Special methods

__str__()

Return string representation of this alignment path.

Special methods (inherited)

__eq__(value, /)	Return self==value.
__ge__(value, /)	Return self>=value.
__getstate__(/)	Helper for pickle.
__gt__(value, /)	Return self>value.
__hash__(/)	Return hash(self).
__le__(value, /)	Return self<=value.
__lt__(value, /)	Return self<value.
__ne__(value, /)	Return self!=value.

Details

__str__()

Return string representation of this alignment path.