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ekingery's solution

to Hamming in the Python Track

Published at Jul 13 2018 · 0 comments
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 Distance between two DNA strands.

Your body is made up of cells that contain DNA. Those cells regularly wear out and need replacing, which they achieve by dividing into daughter cells. In fact, the average human body experiences about 10 quadrillion cell divisions in a lifetime!

When cells divide, their DNA replicates too. Sometimes during this process mistakes happen and single pieces of DNA get encoded with the incorrect information. If we compare two strands of DNA and count the differences between them we can see how many mistakes occurred. This is known as the "Hamming Distance".

We read DNA using the letters C,A,G and T. Two strands might look like this:

GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^  ^ ^    ^^

They have 7 differences, and therefore the Hamming Distance is 7.

The Hamming Distance is useful for lots of things in science, not just biology, so it's a nice phrase to be familiar with :)

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.

Exception messages

Sometimes it is necessary to raise an exception. When you do this, you should include a meaningful error message to indicate what the source of the error is. This makes your code more readable and helps significantly with debugging. Not every exercise will require you to raise an exception, but for those that do, the tests will only pass if you include a message.

To raise a message with an exception, just write it as an argument to the exception type. For example, instead of raise Exception, you should write:

raise Exception("Meaningful message indicating the source of the error")

Running the tests

To run the tests, run the appropriate command below (why they are different):

  • Python 2.7: py.test hamming_test.py
  • Python 3.4+: pytest hamming_test.py

Alternatively, you can tell Python to run the pytest module (allowing the same command to be used regardless of Python version): python -m pytest hamming_test.py

Common pytest options

  • -v : enable verbose output
  • -x : stop running tests on first failure
  • --ff : run failures from previous test before running other test cases

For other options, see python -m pytest -h

Submitting Exercises

Note that, when trying to submit an exercise, make sure the solution is in the $EXERCISM_WORKSPACE/python/hamming directory.

You can find your Exercism workspace by running exercism debug and looking for the line that starts with Workspace.

For more detailed information about running tests, code style and linting, please see Running the Tests.

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.py

import unittest

import hamming


# Tests adapted from `problem-specifications//canonical-data.json` @ v2.3.0

class HammingTest(unittest.TestCase):

    def test_empty_strands(self):
        self.assertEqual(hamming.distance("", ""), 0)

    def test_single_letter_identical_strands(self):
        self.assertEqual(hamming.distance("A", "A"), 0)

    def test_single_letter_different_strands(self):
        self.assertEqual(hamming.distance("G", "T"), 1)

    def test_long_identical_strands(self):
        self.assertEqual(hamming.distance("GGACTGAAATCTG", "GGACTGAAATCTG"), 0)

    def test_long_different_strands(self):
        self.assertEqual(hamming.distance("GGACGGATTCTG", "AGGACGGATTCT"), 9)

    def test_disallow_first_strand_longer(self):
        with self.assertRaisesWithMessage(ValueError):
            hamming.distance("AATG", "AAA")

    def test_disallow_second_strand_longer(self):
        with self.assertRaisesWithMessage(ValueError):
            hamming.distance("ATA", "AGTG")

    def test_disallow_left_empty_strand(self):
        with self.assertRaisesWithMessage(ValueError):
            hamming.distance("", "G")

    def test_disallow_right_empty_strand(self):
        with self.assertRaisesWithMessage(ValueError):
            hamming.distance("G", "")

    # Utility functions
    def setUp(self):
        try:
            self.assertRaisesRegex
        except AttributeError:
            self.assertRaisesRegex = self.assertRaisesRegexp

    def assertRaisesWithMessage(self, exception):
        return self.assertRaisesRegex(exception, r".+")


if __name__ == '__main__':
    unittest.main()
# python solution for hamming test
def distance(strand1='', strand2=''):
    diffs = [1 for a, b in zip(strand1, strand2) if a != b]
    return sum(diffs)

What can you learn from this solution?

A huge amount can be learned 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 you could read more about to improve your understanding?