http://rosalind.info/problems/mprt/
Write a Python program called mprt.py that will accept file of sequence IDs, will download the sequences from UniProt, and will print each protein containing the N-glycosylation motif and a list of the locations where the motif can be found.
The program should print a "usage" statement for -h or --help flags:
$ ./mprt.py -h
usage: mprt.py [-h] [-d DIR] FILE
Find location of N-glycosylation motif
positional arguments:
FILE Input text file of UniProt IDs
optional arguments:
-h, --help show this help message and exit
-d DIR, --download_dir DIR
Directory for downloads (default: fasta)
The input file will list the sequence IDs:
$ cat tests/inputs/1.txt
A2Z669
B5ZC00
P07204_TRBM_HUMAN
P20840_SAG1_YEAST
The output for this file would look like this:
$ ./mprt.py tests/inputs/1.txt
B5ZC00
85 118 142 306 395
P07204_TRBM_HUMAN
47 115 116 382 409
P20840_SAG1_YEAST
79 109 135 248 306 348 364 402 485 501 614
A passing test suite looks like this:
$ make test
python3 -m pytest -xv --disable-pytest-warnings --flake8 --pylint
--pylint-rcfile=../pylintrc --mypy mprt.py tests/mprt_test.py
============================= test session starts ==============================
...
collected 11 items
mprt.py::FLAKE8 SKIPPED [ 8%]
mprt.py::mypy PASSED [ 16%]
mprt.py::test_find_motif PASSED [ 25%]
mprt.py::test_find_kmers PASSED [ 33%]
tests/mprt_test.py::FLAKE8 SKIPPED [ 41%]
tests/mprt_test.py::mypy PASSED [ 50%]
tests/mprt_test.py::test_exists PASSED [ 58%]
tests/mprt_test.py::test_usage PASSED [ 66%]
tests/mprt_test.py::test_bad_file PASSED [ 75%]
tests/mprt_test.py::test_1 PASSED [ 83%]
tests/mprt_test.py::test_2 PASSED [ 91%]
::mypy PASSED [100%]
===================================== mypy =====================================
Success: no issues found in 2 source files
======================== 10 passed, 2 skipped in 1.41s =========================
Ken Youens-Clark [email protected]