http://rosalind.info/problems/orf/
Write a Python program called "orf.py" that accepts a FASTA formatted input file as a single positional argument and will print all the possible proteins that could be translated from the open reading frames.
The program should print a "usage" statement for "-h" or "--help" flags:
$ ./orf.py -h
usage: orf.py [-h] FILE
Find ORFs
positional arguments:
FILE Input FASTA file
optional arguments:
-h, --help show this help message and exit
Here is an example input:
$ cat tests/inputs/1.fa
>Rosalind_99
AGCCATGTAGCTAACTCAGGTTACATGGGGATGACCCCGCGACTTGGATTAGAGTCTC\
TTTTGGAATAAGCCTGAATGATCCGAGTAGCATCTCAG
The output given this input file
$ ./orf.py tests/inputs/1.fa
M
MGMTPRLGLESLLE
MLLGSFRLIPKETLIQVAGSSPCNLS
MTPRLGLESLLE
A passing test suite looks like this:
$ make test
python3 -m pytest -xv --disable-pytest-warnings --flake8 --pylint --mypy orf.py tests/orf_test.py
============================ test session starts ============================
...
orf.py::FLAKE8 SKIPPED [ 7%]
orf.py::mypy PASSED [ 15%]
orf.py::test_find_orfs PASSED [ 23%]
orf.py::test_find_codons PASSED [ 30%]
orf.py::test_translate PASSED [ 38%]
tests/orf_test.py::FLAKE8 PASSED [ 46%]
tests/orf_test.py::mypy PASSED [ 53%]
tests/orf_test.py::test_exists PASSED [ 61%]
tests/orf_test.py::test_usage PASSED [ 69%]
tests/orf_test.py::test_ok1 PASSED [ 76%]
tests/orf_test.py::test_ok2 PASSED [ 84%]
tests/orf_test.py::test_ok3 PASSED [ 92%]
::mypy PASSED [100%]
=================================== mypy ====================================
Success: no issues found in 2 source files
======================= 12 passed, 1 skipped in 2.07s =======================
Ken Youens-Clark [email protected]