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
--pylint-rcfile=../pylintrc --mypy orf.py tests/orf_test.py
============================= test session starts ==============================
...
collected 13 items
orf.py::FLAKE8 PASSED [ 7%]
orf.py::mypy PASSED [ 14%]
orf.py::test_truncate PASSED [ 21%]
orf.py::test_find_orfs PASSED [ 28%]
tests/orf_test.py::FLAKE8 SKIPPED [ 35%]
tests/orf_test.py::mypy PASSED [ 42%]
tests/orf_test.py::test_exists PASSED [ 50%]
tests/orf_test.py::test_usage PASSED [ 57%]
tests/orf_test.py::test_bad_file PASSED [ 64%]
tests/orf_test.py::test_empty PASSED [ 71%]
tests/orf_test.py::test_ok1 PASSED [ 78%]
tests/orf_test.py::test_ok2 PASSED [ 85%]
tests/orf_test.py::test_ok3 PASSED [ 92%]
::mypy PASSED [100%]
===================================== mypy =====================================
Success: no issues found in 2 source files
======================== 13 passed, 1 skipped in 1.75s =========================
Ken Youens-Clark [email protected]