Instructions

Test suite

Solution

Note:

This solution was written on an old version of Exercism. The tests below might not correspond to the solution code, and the exercise may have changed since this code was written.

Calculate the Hamming difference between two DNA strands.

A mutation is simply a mistake that occurs during the creation or copying of a nucleic acid, in particular DNA. Because nucleic acids are vital to cellular functions, mutations tend to cause a ripple effect throughout the cell. Although mutations are technically mistakes, a very rare mutation may equip the cell with a beneficial attribute. In fact, the macro effects of evolution are attributable by the accumulated result of beneficial microscopic mutations over many generations.

The simplest and most common type of nucleic acid mutation is a point mutation, which replaces one base with another at a single nucleotide.

By counting the number of differences between two homologous DNA strands taken from different genomes with a common ancestor, we get a measure of the minimum number of point mutations that could have occurred on the evolutionary path between the two strands.

This is called the 'Hamming distance'.

It is found by comparing two DNA strands and counting how many of the nucleotides are different from their equivalent in the other string.

GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^  ^ ^    ^^

The Hamming distance between these two DNA strands is 7.

Implementation notes

The Hamming distance is only defined for sequences of equal length. This means that based on the definition, each language could deal with getting sequences of equal length differently.

For installation and learning resources, refer to the exercism help page.

For running the tests provided, you will need the Minitest gem. Open a terminal window and run the following command to install minitest:

gem install minitest

If you would like color output, you can require 'minitest/pride' in the test file, or note the alternative instruction, below, for running the test file.

Run the tests from the exercise directory using the following command:

ruby hamming_test.rb

To include color from the command line:

ruby -r minitest/pride hamming_test.rb

Source

The Calculating Point Mutations problem at Rosalind http://rosalind.info/problems/hamm/

Submitting Incomplete Solutions

It's possible to submit an incomplete solution so you can see how others have completed the exercise.

hamming_test.rb

require 'minitest/autorun'
require_relative 'hamming'

# Common test data version: 2.0.1 f79dfd7
class HammingTest < Minitest::Test
  def test_empty_strands
    # skip
    assert_equal 0, Hamming.compute('', '')
  end

  def test_identical_strands
    skip
    assert_equal 0, Hamming.compute('A', 'A')
  end

  def test_long_identical_strands
    skip
    assert_equal 0, Hamming.compute('GGACTGA', 'GGACTGA')
  end

  def test_complete_distance_in_single_nucleotide_strands
    skip
    assert_equal 1, Hamming.compute('A', 'G')
  end

  def test_complete_distance_in_small_strands
    skip
    assert_equal 2, Hamming.compute('AG', 'CT')
  end

  def test_small_distance_in_small_strands
    skip
    assert_equal 1, Hamming.compute('AT', 'CT')
  end

  def test_small_distance
    skip
    assert_equal 1, Hamming.compute('GGACG', 'GGTCG')
  end

  def test_small_distance_in_long_strands
    skip
    assert_equal 2, Hamming.compute('ACCAGGG', 'ACTATGG')
  end

  def test_non_unique_character_in_first_strand
    skip
    assert_equal 1, Hamming.compute('AAG', 'AAA')
  end

  def test_non_unique_character_in_second_strand
    skip
    assert_equal 1, Hamming.compute('AAA', 'AAG')
  end

  def test_same_nucleotides_in_different_positions
    skip
    assert_equal 2, Hamming.compute('TAG', 'GAT')
  end

  def test_large_distance
    skip
    assert_equal 4, Hamming.compute('GATACA', 'GCATAA')
  end

  def test_large_distance_in_off_by_one_strand
    skip
    assert_equal 9, Hamming.compute('GGACGGATTCTG', 'AGGACGGATTCT')
  end

  def test_disallow_first_strand_longer
    skip
    assert_raises(ArgumentError) { Hamming.compute('AATG', 'AAA') }
  end

  def test_disallow_second_strand_longer
    skip
    assert_raises(ArgumentError) { Hamming.compute('ATA', 'AGTG') }
  end

  # Problems in exercism evolve over time, as we find better ways to ask
  # questions.
  # The version number refers to the version of the problem you solved,
  # not your solution.
  #
  # Define a constant named VERSION inside of the top level BookKeeping
  # module, which may be placed near the end of your file.
  #
  # In your file, it will look like this:
  #
  # module BookKeeping
  #   VERSION = 1 # Where the version number matches the one in the test.
  # end
  #
  # If you are curious, read more about constants on RubyDoc:
  # http://ruby-doc.org/docs/ruby-doc-bundle/UsersGuide/rg/constants.html

  def test_bookkeeping
    skip
    assert_equal 3, BookKeeping::VERSION
  end
end

class Hamming
  def self.compute(strand1, strand2)
    raise ArgumentError, "Arguments length is not equal" unless
      strand1.length == strand2.length

    strands   = strand1.chars.zip(strand2.chars)
    different = proc { |n1, n2| n1 != n2 }

    strands.count(&different)
  end
end

module BookKeeping
  VERSION = 3
end

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to Hamming in the Ruby Track