http://rosalind.info/problems/hamm/
Write a Python program called hamm.py that takes a single position argument which is a readable file that will contain two lines of DNA sequences and will print the Hamming distance between them.
The program should print a "usage" statement for -h or --help flags:
$ ./hamm.py -h
usage: hamm.py [-h] FILE
Hamming distance
positional arguments:
FILE File input
optional arguments:
-h, --help show this help message and exit
Here is an example input file:
$ cat tests/inputs/1.txt
GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
The output should be an integer value, for instance, 7 here as 7 bases would need to be changed to transform one sequence to the other:
$ ./hamm.py tests/inputs/1.txt
7
A passing test suite looks like this:
$ make test
python3 -m pytest -xv --disable-pytest-warnings --flake8 --pylint
--mypy hamm.py tests/hamm_test.py
============================ test session starts ============================
...
hamm.py::FLAKE8 SKIPPED [ 8%]
hamm.py::mypy PASSED [ 16%]
hamm.py::test_hamming PASSED [ 25%]
tests/hamm_test.py::FLAKE8 SKIPPED [ 33%]
tests/hamm_test.py::mypy PASSED [ 41%]
tests/hamm_test.py::test_exists PASSED [ 50%]
tests/hamm_test.py::test_usage PASSED [ 58%]
tests/hamm_test.py::test_bad_file PASSED [ 66%]
tests/hamm_test.py::test_input1 PASSED [ 75%]
tests/hamm_test.py::test_input2 PASSED [ 83%]
tests/hamm_test.py::test_empty_file PASSED [ 91%]
::mypy PASSED [100%]
=================================== mypy ====================================
Success: no issues found in 2 source files
======================= 10 passed, 2 skipped in 0.40s =======================
Ken Youens-Clark [email protected]