ruby - 如何编写一个方法来计算 ruby​​ 中字符串中最常见的子字符串？

Question

我的程序具有类 DNA。该程序计算字符串中出现频率最高的 k-mer。因此，它正在寻找长度为 k 的字符串中最常见的子字符串。

一个例子是创建一个带有 AACCAATCCG 字符串的 dna1 对象。 count k-mer 方法将查找长度为 k 的子串并输出最常见的答案。所以，如果我们设置 k = 1 那么 'A' 和 'C' 将是字符串中出现次数最多的，因为它出现了四次。请参见下面的示例:

 dna1 = DNA.new('AACCAATCCG')
=> AACCAATCCG
>> dna1.count_kmer(1)
=> [#<Set: {"A", "C"}>, 4]
>> dna1.count_kmer(2)
=> [#<Set: {"AA", "CC"}>, 2]

这是我的 DNA 类:

   class DNA
      def initialize (nucleotide)
        @nucleotide = nucleotide
      end
      def length
        @nucleotide.length
      end   
      protected
 attr_reader :nucleotide
end

这是我尝试实现的 count kmer 方法:

# I have k as my only parameter because I want to pass the nucleotide string in the method
def count_kmer(k)

# I created an array as it seems like a good way to split up the nucleotide string.
  counts = []

  #this tries to count how many kmers of length k there are
  num_kmers = self.nucleotide.length- k + 1

  #this should try and look over the kmer start positions
  for i in num_kmers

    #Slice the string, so that way we can get the kmer
    kmer = self.nucleotide.split('')
  end

  #add kmer if its not present
  if !kmer = counts
    counts[kmer] = 0

    #increment the count for kmer
    counts[kmer] +=1 
  end

  #return the final count
return counts
end

#end dna class
end

我不确定我的方法哪里出了问题。

Answer 1

是这样的吗？

  require 'set'

  def count_kmer(k)
    max_kmers = kmers(k)
                    .each_with_object(Hash.new(0)) { |value, count| count[value] += 1 }
                    .group_by { |_,v| v }
                    .max
    [Set.new(max_kmers[1].map { |e| e[0] }), max_kmers[0]]
  end

  def kmers(k)
    nucleotide.chars.each_cons(k).map(&:join)
  end

编辑:这是类(class)的全文:

require 'set'

class DNA
  def initialize (nucleotide)
    @nucleotide = nucleotide
  end

  def length
    @nucleotide.length
  end

  def count_kmer(k)
    max_kmers = kmers(k)
                    .each_with_object(Hash.new(0)) { |value, count| count[value] += 1 }
                    .group_by { |_,v| v }
                    .max
    [Set.new(max_kmers[1].map { |e| e[0] }), max_kmers[0]]
  end

  def kmers(k)
    nucleotide.chars.each_cons(k).map(&:join)
  end

  protected
  attr_reader :nucleotide
end

这会产生以下输出，使用 Ruby 2.2.1，使用您指定的类和方法:

>> dna1 = DNA.new('AACCAATCCG')
=> #<DNA:0x007fe15205bc30 @nucleotide="AACCAATCCG">
>> dna1.count_kmer(1)
=> [#<Set: {"A", "C"}>, 4]
>> dna1.count_kmer(2)
=> [#<Set: {"AA", "CC"}>, 2]

作为奖励，您还可以:

>> dna1.kmers(2)
=> ["AA", "AC", "CC", "CA", "AA", "AT", "TC", "CC", "CG"]