Sequence Aligner¶
Module for handling sequence alignment.

class
yalign.sequencealigner.
SequenceAligner
(score, gap_penalty)¶ Bases:
object
Aligns two sequences.

class
yalign.sequencealigner.
SequenceAlignmentSearchProblem
(xs, ys, score, gap_penalty)¶ Bases:
simpleai.search.models.SearchProblem
Represents and manipulates the search space for a sequence alignment problem. Used by simpleai’s graph search algorithm.

actions
(state)¶ Returns the next actions from a given state. A state is an alignment (tuple of indexes from either sequence). An action is a the next alignment to consider with a score for that alignment.

cost
(state1, action, state2)¶ Cost of this action.

heuristic
(state)¶ A heuristic for A* type searches. Currently we return The distance of this state from the diagonal in a N*M lattice where N and M are the lengths of the two sequences.

is_goal
(state)¶ Are we finished aligning? True when our when state is the alignment (N, M) where N and M are the lengths of the two sequences.

result
(state, action)¶ Returns the next state for this state, action pair.
