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 :)
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.
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")
To run the tests, run
Alternatively, you can tell Python to run the pytest module:
python -m pytest hamming_test.py
-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
Note that, when trying to submit an exercise, make sure the solution is in the
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exercism debug and looking for the line that starts with
For more detailed information about running tests, code style and linting, please see Running the Tests.
The Calculating Point Mutations problem at Rosalind http://rosalind.info/problems/hamm/
It's possible to submit an incomplete solution so you can see how others have completed the exercise.
import unittest from hamming import distance # Tests adapted from `problem-specifications//canonical-data.json` class HammingTest(unittest.TestCase): def test_empty_strands(self): self.assertEqual(distance("", ""), 0) def test_single_letter_identical_strands(self): self.assertEqual(distance("A", "A"), 0) def test_single_letter_different_strands(self): self.assertEqual(distance("G", "T"), 1) def test_long_identical_strands(self): self.assertEqual(distance("GGACTGAAATCTG", "GGACTGAAATCTG"), 0) def test_long_different_strands(self): self.assertEqual(distance("GGACGGATTCTG", "AGGACGGATTCT"), 9) def test_disallow_first_strand_longer(self): with self.assertRaisesWithMessage(ValueError): distance("AATG", "AAA") def test_disallow_second_strand_longer(self): with self.assertRaisesWithMessage(ValueError): distance("ATA", "AGTG") def test_disallow_left_empty_strand(self): with self.assertRaisesWithMessage(ValueError): distance("", "G") def test_disallow_right_empty_strand(self): with self.assertRaisesWithMessage(ValueError): distance("G", "") # Utility functions def assertRaisesWithMessage(self, exception): return self.assertRaisesRegex(exception, r".+") if __name__ == "__main__": unittest.main()
VALID_DNA_BASES = ['A', 'T', 'G', 'C'] def distance(strand1, strand2): """Calculate the Hamming distance between two DNA strands.""" if len(strand1) != len(strand2): raise ValueError('Cannot get the hamming distance - strands are of different lengths') max_distance = len(strand1) final_distance = 0 for idx in range(0, max_distance): if strand1[idx] not in VALID_DNA_BASES: raise ValueError if strand2[idx] not in VALID_DNA_BASES: raise ValueError if strand1[idx] != strand2[idx]: final_distance = final_distance + 1 return final_distance
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.