Module distance

Compute the Levenshtein distance between two sequences. By default, will compare the elements using the == operator, but any binary function can be given as the equality argument.

delins_cost is the cost applied for deletions and insertions.

subst_cost_fun is a binary function that gives the cost to substitute the first argument with the second. If not given, a cost of delins is used for any substitution.

Compute the Levenshtein distance between two sequences. This does the same thing as levenshtein_distance, but stores pointers to indicate what alignments gave the costs and returns the full cost matrix, plus the pointer matrix.

seq2 is aligned with seq1: that is, a deletion indicates that seq1 moves on a cell without a corresponding cell in seq2.

Finds the optimal alignment of the two sequences using Levenshtein distance and traces back the pointers to find the alignment. Returns a list of pairs, containing the points from the two lists.

In the case of a substitution, it will contain the two points that were aligned. In the case of an insertion, the first value will be None and the second the inserted value. In the case of a deletion, the second value will be None and the first the deleted value.

Note that the pair of values in the case of a substitution may be equal - an alignment - or not - a substitution - depending on the substitution cost function.

Parameters:

• dist (bool) - return a tuple of the alignment and the dist

Compute a local alignment variant of the Levenshtein distance between two sequences. Options are the same as levenshtein_distance_with_pointers.

Finds the optimal alignment of seq2 within seq1.

In addition to the operations I, D and S used in levenshtein_distance_with_pointers, we use here '.' to indicate a deletion at zero-cost at the beginning or end.