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82 lines
3.2 KiB
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82 lines
3.2 KiB
Markdown
# Hamming
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Calculate the Hamming Distance between two DNA strands.
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Your body is made up of cells that contain DNA. Those cells regularly
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wear out and need replacing, which they achieve by dividing into
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daughter cells. In fact, the average human body experiences about 10
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quadrillion cell divisions in a lifetime!
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When cells divide, their DNA replicates too. Sometimes during this
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process mistakes happen and single pieces of DNA get encoded with the
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incorrect information. If we compare two strands of DNA and count the
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differences between them we can see how many mistakes occurred. This is
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known as the "Hamming Distance".
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We read DNA using the letters C,A,G and T. Two strands might look like this:
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GAGCCTACTAACGGGAT
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CATCGTAATGACGGCCT
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^ ^ ^ ^ ^ ^^
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They have 7 differences, and therefore the Hamming Distance is 7.
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The Hamming Distance is useful for lots of things in science, not just biology,
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so it's a nice phrase to be familiar with :)
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# Implementation notes
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The Hamming distance is only defined for sequences of equal length, so
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an attempt to calculate it between sequences of different lengths should
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not work. The general handling of this situation (e.g., raising an
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exception vs returning a special value) may differ between languages.
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## Exception messages
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Sometimes it is necessary to raise an exception. When you do this, you should include a meaningful error message to
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indicate what the source of the error is. This makes your code more readable and helps significantly with debugging. Not
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every exercise will require you to raise an exception, but for those that do, the tests will only pass if you include
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a message.
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To raise a message with an exception, just write it as an argument to the exception type. For example, instead of
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`raise Exception`, you should write:
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```python
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raise Exception("Meaningful message indicating the source of the error")
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```
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## Running the tests
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To run the tests, run the appropriate command below ([why they are different](https://github.com/pytest-dev/pytest/issues/1629#issue-161422224)):
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- Python 2.7: `py.test hamming_test.py`
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- Python 3.4+: `pytest hamming_test.py`
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Alternatively, you can tell Python to run the pytest module (allowing the same command to be used regardless of Python version):
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`python -m pytest hamming_test.py`
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### Common `pytest` options
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- `-v` : enable verbose output
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- `-x` : stop running tests on first failure
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- `--ff` : run failures from previous test before running other test cases
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For other options, see `python -m pytest -h`
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## Submitting Exercises
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Note that, when trying to submit an exercise, make sure the solution is in the `$EXERCISM_WORKSPACE/python/hamming` directory.
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You can find your Exercism workspace by running `exercism debug` and looking for the line that starts with `Workspace`.
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For more detailed information about running tests, code style and linting,
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please see [Running the Tests](http://exercism.io/tracks/python/tests).
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## Source
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The Calculating Point Mutations problem at Rosalind [http://rosalind.info/problems/hamm/](http://rosalind.info/problems/hamm/)
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## Submitting Incomplete Solutions
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It's possible to submit an incomplete solution so you can see how others have completed the exercise.
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