http://rosalind.info/problems/gc/
Write a Python program called cgc.py that takes a single positional argument which should be a readable text file.
The program should print a "usage" statement for -h or --help flags:
$ ./cgc.py -h
usage: cgc.py [-h] FILE
Compute GC content
positional arguments:
FILE Input sequence file
optional arguments:
-h, --help show this help message and exit
The input file will be in FASTA format:
$ cat tests/inputs/1.fa
>Rosalind_6404
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCC
TCCCACTAATAATTCTGAGG
>Rosalind_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCT
ATATCCATTTGTCAGCAGACACGC
>Rosalind_0808
CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGAC
TGGGAACCTGCGGGCAGTAGGTGGAAT
The output should be the sequence ID with the highest GC content along with that GC content as a floating-point value to 6 significant digits:
$ ./cgc.py tests/inputs/1.fa
Rosalind_0808 60.919540
A fully passing test suite looks like the following:
$ make test
python3 -m pytest -xv --disable-pytest-warnings --flake8 --pylint
--mypy cgc.py tests/cgc_test.py
============================ test session starts ============================
...
cgc.py::FLAKE8 SKIPPED [ 9%]
cgc.py::mypy PASSED [ 18%]
cgc.py::test_gc PASSED [ 27%]
tests/cgc_test.py::FLAKE8 SKIPPED [ 36%]
tests/cgc_test.py::mypy PASSED [ 45%]
tests/cgc_test.py::test_exists PASSED [ 54%]
tests/cgc_test.py::test_usage PASSED [ 63%]
tests/cgc_test.py::test_bad_input PASSED [ 72%]
tests/cgc_test.py::test_good_input1 PASSED [ 81%]
tests/cgc_test.py::test_good_input2 PASSED [ 90%]
::mypy PASSED [100%]
=================================== mypy ====================================
Success: no issues found in 2 source files
======================= 9 passed, 2 skipped in 1.39s ========================
Ken Youens-Clark [email protected]