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# skbio.alignment.PairAlignPath

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

  Create a pairwise alignment path from segment lengths and states.

  Parameters:
    lengths array_like of int of shape (n_segments,)

      Length of each segment in the alignment.

    states array_like of uint8 of shape (n_segments,)

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

    starts array_like of (int, int), optional

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

  See also

  `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) | Create a pairwise alignment path from a bit array.
  `from_cigar`(cigar[, starts]) | Create a pairwise alignment path from a CIGAR string.
  `to_bits`() | Unpack states into an array of bits.
  `to_cigar`([seqs]) | Generate a CIGAR string representing the pairwise alignment path.

  Methods (inherited)

  `from_coordinates`(coords) | Generate 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.
  `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 AlignPath.

  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 AlignPath.