agglovar.seqmatch
=================

.. py:module:: agglovar.seqmatch

.. autoapi-nested-parse::

   Fast Smith-waterman implementation.



Classes
-------

.. autoapisummary::

   agglovar.seqmatch.MatchScoreModel


Module Contents
---------------

.. py:class:: MatchScoreModel

   An engine for scoring alignments.

   Intended for determining sequence similarity through an alignment where the alignment itself is
   not important.

   :param match: Base match score (> 0.0).
   :param mismatch: Base mismatch score (< 0.0).
   :param gap_open: Gap open cost (<= 0.0).
   :param gap_extend: Gap extend cost (<= 0.0).
   :param map_limit: Maximum sequence size before falling back to Jaccard index in :func:`match_prop()`.
   :param jaccard_kmer: Jaccard k-mer size for comparisons falling back to Jaccard index in
       :func:`match_prop()`.


   .. py:method:: __post_init__() -> None

      Post-initialization.



   .. py:method:: match_prop(seq_a: str, seq_b: str) -> float

      Get the alignment score proportion over the max possible score between two sequences.

      To follow tandem duplications to map correctly, seq_b is duplicated head-to-tail
      (seq_b + seq_b) and seq_a is aligned to it.

      The max possible score is achieved if seq_a and seq_b are the same size and seq_a aligns to
      seq_b + seq_b with all seq_a bases matching (function returns 1.0).

      The numerator is the alignment score and the denominator is the size of the larger sequence times the match

      score::

          min(
              score_align(seq_a, seq_b + seq_b), min_len(seq_a, seq_b) * match
          ) / (
              max_len(seq_a, seq_b) * match
          )

      :param seq_a: Subject sequence.
      :param seq_b: Query sequence.

      :returns: Alignment proportion with seq_b duplicated head to tail. If either sequence is
          None or empty, returns 0.0



   .. py:method:: score_align(seq_a: str, seq_b: str) -> float

      Get max score aligning two sequences.

      Only returns the score, not the alignment.

      This is a legacy native Python implementation used by SV-Pop. It is accurate, but extremely slow.

      :param seq_a: Subject sequence.
      :param seq_b: Query sequence.


      :returns: Maximum alignment score.



   .. py:method:: score_align_native(seq_a: str, seq_b: str) -> float

      Get max score aligning two sequences.

      Only returns the score, not the alignment.commands = [["pytest", "{posargs}"]]

      This is a legacy native Python implementation used by SV-Pop. It is validated, but extremely slow.

      :param seq_a: Subject sequence.
      :param seq_b: Query sequence.

      :returns: Maximum alignment score.



   .. py:attribute:: affine_gap
      :type:  float


   .. py:attribute:: jaccard_kmer
      :type:  int
      :value: 9



   .. py:attribute:: map_limit
      :type:  Optional[int]
      :value: 5000



   .. py:attribute:: match
      :type:  float


   .. py:attribute:: mismatch
      :type:  float


   .. py:attribute:: rotate_min
      :type:  int
      :value: 3



   .. py:attribute:: score_model
      :type:  agglovar.align.score.AffineScoreModel
      :value: None