Hello all,


Here is an attempt at a naive fuzzy string matching algorithm. I would
appreciate comments on the code - which is not as simple as I would
like.

I have a couple of speed improvements in mind:
  1) replace EQUAL hash with array (possibly NArray).
  2) a path can be terminated before fully explored if it can be
calculated that it will never complete (somewhere inside in_bounds?).


Cheers,


Martin



#!/usr/bin/env ruby

require 'pp'

VERBOSE = false
TEST    = true

# IUPAC nucleotide pair ambiguity equivalents
EQUAL = {
  :AA => true, :BU => true, :TH => true, :UY => true,
  :TT => true, :CB => true, :UH => true, :SC => true,
  :CC => true, :GB => true, :VA => true, :SG => true,
  :GG => true, :TB => true, :VC => true, :CS => true,
  :UU => true, :UB => true, :VG => true, :GS => true,
  :NA => true, :DA => true, :AV => true, :WA => true,
  :NT => true, :DG => true, :CV => true, :WT => true,
  :NC => true, :DT => true, :GV => true, :WU => true,
  :NG => true, :DU => true, :KG => true, :AW => true,
  :NU => true, :AD => true, :KT => true, :TW => true,
  :AN => true, :GD => true, :KU => true, :UW => true,
  :TN => true, :TD => true, :GK => true, :RA => true,
  :CN => true, :UD => true, :TK => true, :RG => true,
  :GN => true, :HA => true, :UK => true, :AR => true,
  :UN => true, :HC => true, :YC => true, :GR => true,
  :NN => true, :HT => true, :YT => true, :MA => true,
  :BC => true, :HU => true, :YU => true, :MC => true,
  :BG => true, :AH => true, :CY => true, :AM => true,
  :BT => true, :CH => true, :TY => true, :CM => true,
}

# Class to match two nucleotide sequences allowing for ambiguity codes
# and a given maximum number of matches, insertions, and deletions.
class Matcher
  attr_accessor :seq1_index, :seq2_index, :matches, :mismatches,
:insertions, :deletions

  def initialize(seq1, seq2, max_mismatches = 0, max_insertions = 0,
max_deletions = 0, seq1_index = 0, seq2_index = 0, matches = 0,
mismatches = 0, insertions = 0, deletions = 0)
    @seq1           = seq1
    @seq2           = seq2
    @max_mismatches = max_mismatches
    @max_insertions = max_insertions
    @max_deletions  = max_deletions
    @seq1_index     = seq1_index
    @seq2_index     = seq2_index
    @matches        = matches
    @mismatches     = mismatches
    @insertions     = insertions
    @deletions      = deletions
  end

  # Method to explore all paths for matching two sequences allowing for
  # a given maximum number of mismatches, insertions and deletions.
  def match
    paths = []
    paths << self

    while not paths.empty?
      pp paths if VERBOSE

      new_paths = []

      paths.each do |path|
        if path.match?                               # ---- Match ----
          path_matches = path.dup
          path_matches.matches += 1

          return path_matches if path_matches.ok?

          path_matches.seq1_index += 1
          path_matches.seq2_index += 1

          new_paths << path_matches if path_matches.in_bounds?
        else                                         # ---- Mismatch
----
          path_mismatches = path.dup
          path_mismatches.mismatches += 1

          return path_mismatches if path_mismatches.ok?

          path_mismatches.seq1_index += 1
          path_mismatches.seq2_index += 1

          new_paths << path_mismatches if path_mismatches.in_bounds?
        end

        if path.insertions < @max_insertions         # ---- Insertion
----
          path_insertions = path.dup
          path_insertions.insertions += 1

          return path_insertions if path_insertions.ok?

          path_insertions.seq1_index += 1

          new_paths << path_insertions if path_insertions.in_bounds?
        end

        if path.deletions < @max_deletions           # ---- Deletion
----
          path_deletions = path.dup
          path_deletions.deletions += 1

          return path_deletions if path_deletions.ok?

          path_deletions.seq2_index += 1

          new_paths << path_deletions if path_deletions.in_bounds?
        end
      end

      paths = new_paths
    end
  end

  # Method to check if residues match.
  def match?
    if self.seq1_index < @seq1.length and self.seq2_index < @seq2.length
      EQUAL[(@seq1[self.seq1_index].upcase +
@seq2[self.seq2_index].upcase).to_sym]
    end
  end

  # Method to check if a path is complete.
  def ok?
    if self.mismatches <= @max_mismatches and self.insertions <=
@max_insertions and self.deletions <= @max_deletions
      if @seq1.length == self.matches + self.mismatches +
self.insertions and
         @seq2.length == self.matches + self.mismatches + self.deletions
        pp self if VERBOSE
        true
      end
    end
  end

  # Method to check if the path is within the search space.
  def in_bounds?
    if self.seq1_index <= @seq1.length and self.seq2_index <=
@seq2.length
      true
    else
      false
    end
  end
end

if VERBOSE
  m = Matcher.new("atcg", "atcgX", mismatches=0, insertions=0,
deletions=1)
  m.match
end

if TEST and __FILE__ == $PROGRAM_NAME
  require "test/unit"

  class TestMatcher < Test::Unit::TestCase
    def test_perfect_match_returns_ok
      m = Matcher.new("atcg", "atcg", mismatches=0, insertions=0,
deletions=0)
      assert_not_nil(m.match)
    end

    def test_perfect_match_with_ambiguity_returns_ok
      m = Matcher.new("atcg", "NNNN", mismatches=0, insertions=0,
deletions=0)
      assert_not_nil(m.match)
    end

    def test_one_mismatch_with_zero_allowed_returns_nil
      m = Matcher.new("atcg", "atGg", mismatches=0, insertions=0,
deletions=0)
      assert_equal(nil, m.match)
    end

    def test_one_mismatch_with_one_allowed_returns_ok
      m = Matcher.new("atcg", "atGg", mismatches=1, insertions=0,
deletions=0)
      assert_not_nil(m.match)
    end

    def test_two_mismatch_with_one_allowed_returns_nil
      m = Matcher.new("atcg", "GtGg", mismatches=1, insertions=0,
deletions=0)
      assert_equal(nil, m.match)
    end

    def test_two_mismatch_with_two_allowed_returns_ok
      m = Matcher.new("atcg", "GtGg", mismatches=2, insertions=0,
deletions=0)
      assert_not_nil(m.match)
    end

    def test_one_insertion_with_zero_allowed_returns_nil
      m = Matcher.new("atGcg", "atcg", mismatches=0, insertions=0,
deletions=0)
      assert_equal(nil, m.match)
    end

    def test_one_insertion_with_one_allowed_returns_ok
      m = Matcher.new("atGcg", "atcg", mismatches=0, insertions=1,
deletions=0)
      assert_not_nil(m.match)
    end

    def test_two_insertion_with_one_allowed_returns_nil
      m = Matcher.new("atGcgC", "atcg", mismatches=0, insertions=1,
deletions=0)
      assert_equal(nil, m.match)
    end

    def test_two_insertion_with_two_allowed_returns_ok
      m = Matcher.new("atGcgC", "atcg", mismatches=0, insertions=2,
deletions=0)
      assert_not_nil(m.match)
    end

    def test_one_deletion_with_zero_allowed_returns_nil
      m = Matcher.new("atcg", "atcAg", mismatches=0, insertions=0,
deletions=0)
      assert_equal(nil, m.match)
    end

    def test_one_deletion_with_one_allowed_returns_ok
      m = Matcher.new("atcg", "atcAg", mismatches=0, insertions=0,
deletions=1)
      assert_not_nil(m.match)
    end

    def test_two_deletion_with_one_allowed_returns_nil
      m = Matcher.new("atcg", "TatcAg", mismatches=0, insertions=0,
deletions=1)
      assert_equal(nil, m.match)
    end

    def test_two_deletion_with_two_allowed_returns_ok
      m = Matcher.new("atcg", "AatcTg", mismatches=0, insertions=0,
deletions=2)
      assert_not_nil(m.match)
    end

    def test_one_mismatch_one_insertions_one_deletion_returns_ok
      m = Matcher.new("TaGcg", "atcgA", mismatches=1, insertions=1,
deletions=1)
      assert_not_nil(m.match)
    end
  end
end

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