Avatar of davearonson

davearonson's solution

to Hamming in the Python Track

Published at May 19 2019 · 0 comments
Instructions
Test suite
Solution

Note:

This exercise has changed since this solution 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()

hamming.py

# constants so we can use them outside, such as in tests
# pylint: disable=C0326
INVALID_BASE_MESSAGE    = "Invalid base detected"
LENGTH_MISMATCH_MESSAGE = "DNA strands must have the same length"
NOT_STRING_MESSAGE      = "DNA strands must be strings"
VALID_BASES             = "ACGT"


def distance(strand_a, strand_b):

    if not (isinstance(strand_a, str) and isinstance(strand_b, str)):
        raise ValueError(NOT_STRING_MESSAGE)

    if len(strand_a) != len(strand_b): raise ValueError(LENGTH_MISMATCH_MESSAGE)

    for base in strand_a + strand_b:
        if not base in VALID_BASES: raise ValueError(INVALID_BASE_MESSAGE)

    # could make this a oneliner, like:
    # return len([1 for pair in zip(strand_a, strand_b) if pair[0] != pair[1]])
    # but IMHO the clarity is worth the extra lines.
    # also, could use any value; just chose 1 as a placeholder likely to be
    # smaller than storing the actual mismatched pair, and in case i wanted
    # to sum it instead of looking at the length.
    pairs = zip(strand_a, strand_b)
    mismatches = [1 for a,b in pairs if a != b]
    return len(mismatches)

daves_hamming_test.py

import pytest

import hamming

# basic functionality

def test_same_singles_means_distance_zero():
    assert hamming.distance("G", "G") == 0

def test_different_singles_means_distance_one():
    assert hamming.distance("G", "C") == 1

# not much value in testing twos

def test_same_three_means_distance_zero():
    assert hamming.distance("GCA", "GCA") == 0

def test_three_different_at_start_means_distance_one():
    assert hamming.distance("GCA", "CCA") == 1

def test_three_different_in_middle_means_distance_one():
    assert hamming.distance("GCA", "GGA") == 1

def test_three_different_at_end_means_distance_one():
    assert hamming.distance("GCA", "GCG") == 1

def test_three_same_only_at_start_means_distance_two():
    assert hamming.distance("GCA", "GTG") == 2

def test_three_same_only_in_middle_means_distance_two():
    assert hamming.distance("GCA", "TCC") == 2

def test_three_same_only_at_end_means_distance_two():
    assert hamming.distance("GCA", "CGA") == 2

def test_different_three_means_distance_three():
    assert hamming.distance("GCA", "CAG") == 3

# going up to three should be enough to prove the general case

# light bulletproofing: valid edge case

def test_two_empty_means_distance_zero():
    assert hamming.distance("", "") == 0

# medium bulletproofing: invalid edge cases and likely errors

def test_raises_with_msg_if_first_shorter():
    with pytest.raises(ValueError) as exception_info:
        hamming.distance("GC", "TGA")
    assert hamming.LENGTH_MISMATCH_MESSAGE in str(exception_info)

def test_raises_with_msg_if_second_shorter():
    with pytest.raises(ValueError) as exception_info:
        hamming.distance("GCA", "TG")
    assert hamming.LENGTH_MISMATCH_MESSAGE in str(exception_info)

def test_raises_with_msg_if_first_has_invalid_base():
    with pytest.raises(ValueError) as exception_info:
        hamming.distance("CAGE", "CAGT")
    assert hamming.INVALID_BASE_MESSAGE in str(exception_info)

def test_raises_with_msg_if_second_has_invalid_base():
    with pytest.raises(ValueError) as exception_info:
        hamming.distance("CAGT", "CAGE")
    assert hamming.INVALID_BASE_MESSAGE in str(exception_info)

# heavy bulletproofing: invalid cases not likely from innocent error

def test_raises_with_msg_if_first_not_string():
    with pytest.raises(ValueError) as exception_info:
        hamming.distance(3, "TG")
    assert hamming.NOT_STRING_MESSAGE in str(exception_info)

def test_raises_with_msg_if_second_not_string():
    with pytest.raises(ValueError) as exception_info:
        hamming.distance("TG", 3)
    assert hamming.NOT_STRING_MESSAGE in str(exception_info)

hamming_test.py

import unittest

import hamming


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

# pylint: disable=C0103  # haha, unittest doesn't obey pylint's demands!
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()

Community comments

Find this solution interesting? Ask the author a question to learn more.

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?