http://rosalind.info/problems/lcsm/
Write a Python program called lcsm.py that will accept FASTA file of sequences as a single positional argument and will print the longest common subsequence shared by all the sequences.
The program should print a "usage" statement for -h or --help flags:
$ ./lcsm.py -h
usage: lcsm.py [-h] FILE
Longest Common Substring
positional arguments:
FILE Input FASTA
optional arguments:
-h, --help show this help message and exit
The input file will be in FASTA format:
$ cat tests/inputs/1.fa
>Rosalind_1
GATTACA
>Rosalind_2
TAGACCA
>Rosalind_3
ATACA
The output for this file would look like this:
$ ./lcsm.py tests/inputs/1.fa
CA
A passing test suite looks like this:
$ make test
python3 -m pytest -xv --disable-pytest-warnings --flake8 --pylint
--pylint-rcfile=../pylintrc --mypy lcsm.py tests/lcsm_test.py
============================= test session starts ==============================
...
collected 13 items
lcsm.py::FLAKE8 SKIPPED [ 7%]
lcsm.py::mypy PASSED [ 14%]
lcsm.py::test_binary_search PASSED [ 21%]
lcsm.py::test_common_kmers PASSED [ 28%]
lcsm.py::test_find_kmers PASSED [ 35%]
tests/lcsm_test.py::FLAKE8 SKIPPED [ 42%]
tests/lcsm_test.py::mypy PASSED [ 50%]
tests/lcsm_test.py::test_exists PASSED [ 57%]
tests/lcsm_test.py::test_usage PASSED [ 64%]
tests/lcsm_test.py::test_bad_file PASSED [ 71%]
tests/lcsm_test.py::test_short PASSED [ 78%]
tests/lcsm_test.py::test_long PASSED [ 85%]
tests/lcsm_test.py::test_no_shared PASSED [ 92%]
::mypy PASSED [100%]
===================================== mypy =====================================
Success: no issues found in 2 source files
======================== 12 passed, 2 skipped in 2.13s =========================
Ken Youens-Clark [email protected]