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4d47's solution

to Hamming in the Ruby Track

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Instructions
Test suite
Solution

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, so an attempt to calculate it between sequences of different lengths should not work. The general handling of this situation (e.g., raising an exception vs returning a special value) may differ between languages.


For installation and learning resources, refer to the Ruby resources 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: 2.1.0 b5d154b
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) do
      Hamming.compute('AATG', 'AAA')
    end
  end

  def test_disallow_second_strand_longer
    skip
    assert_raises(ArgumentError) do
      Hamming.compute('ATA', 'AGTG')
    end
  end
end
class Hamming
  def self.compute(a, b)
    raise ArgumentError, 'strand sequences must be of equal length' unless a.length == b.length
    (0...a.length).count { |i| a[i] != b[i] }
  end

end

module BookKeeping
  VERSION = 3
end

What can you learn from this solution?

A huge amount can be learnt from reading other people’s code. This is why we wanted to give exercism users the option of making their solutions public.

Here are some questions to help you reflect on this solution and learn the most from it.

  • What compromises have been made?
  • Are there new concepts here that I could read more about to develop my understanding?