Module: BioDSL::Dynamic

Extended by:
Ambiguity
Defined in:
lib/BioDSL/seq/dynamic.rb

Overview

Module containing code to locate nucleotide patterns in sequences allowing for ambiguity codes and a given maximum edit distance. Insertions are nucleotides found in the pattern but not in the sequence. Deletions are nucleotides found in the sequence but not in the pattern.

Inspired by the paper by Bruno Woltzenlogel Paleo (page 197): www.logic.at/people/bruno/Papers/2007-GATE-ESSLLI.pdf

Defined Under Namespace

Classes: Match

Instance Method Summary collapse

Methods included from Ambiguity

add_ambiguity_macro

Instance Method Details

#patmatch(pattern, pos = 0, max_edit_distance = 0) ⇒ Object 

str.patmatch(pattern[, pos[, max_edit_distance]])
-> Match or nil
str.patscan(pattern[, pos[, max_edit_distance]]) { |match|
  block
}
-> Match

Method to iterate through a sequence to locate the first pattern match starting from a given position and allowing for a maximum edit distance.



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# File 'lib/BioDSL/seq/dynamic.rb', line 53

def patmatch(pattern, pos = 0, max_edit_distance = 0)
  patscan(pattern, pos, max_edit_distance) do |m|
    return m
  end
end

#patscan(pattern, pos = 0, max_edit_distance = 0) ⇒ Object 

str.patscan(pattern[, pos[, max_edit_distance]])
-> Array or nil
str.patscan(pattern[, pos[, max_edit_distance]]) { |match|
  block
}
-> Match

Method to iterate through a sequence to locate pattern matches starting from a given position and allowing for a maximum edit distance. Matches found in block context return the Match object. Otherwise matches are returned in an Array.



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# File 'lib/BioDSL/seq/dynamic.rb', line 72

def patscan(pattern, pos = 0, max_edit_distance = 0)
  matches = []

  while (result = match_C(@seq, length, pattern, pattern.length, pos,
                          max_edit_distance))
    match = Match.new(*result, @seq[result[0]...result[0] + result[1]])

    if block_given?
      yield match
    else
      matches << match
    end

    pos = match.beg + 1
  end

  return matches unless block_given?
end