Overlap Graphs

http://rosalind.info/problems/grph/

Write a Python program called grph.py an input file of sequences and an optional overlap size and will print all the pairs of sequences which can be joined given the overlap size.

The program should print a "usage" statement for -h or --help flags:

$ ./grph.py -h
usage: grph.py [-h] [-k size] [-d] FILE

Graph through sequences

positional arguments:
  FILE                  FASTA file

optional arguments:
  -h, --help            show this help message and exit
  -k size, --overlap size
                        Size of overlap (default: 3)
  -d, --debug           Debug (default: False)

The input file will be in FASTA format:

$ cat tests/inputs/1.fa
>Rosalind_0498
AAATAAA
>Rosalind_2391
AAATTTT
>Rosalind_2323
TTTTCCC
>Rosalind_0442
AAATCCC
>Rosalind_5013
GGGTGGG

The output for this file would look like this:

$ ./grph.py tests/inputs/1.fa
Rosalind_0498 Rosalind_2391
Rosalind_0498 Rosalind_0442
Rosalind_2391 Rosalind_2323

A passing test suite looks like this:

$ make test
python3 -m pytest -xv --disable-pytest-warnings --flake8 --pylint --mypy grph.py tests/grph_test.py
============================ test session starts ============================
...

grph.py::FLAKE8 PASSED                                                [  5%]
grph.py::mypy PASSED                                                  [ 10%]
grph.py::test_find_kmers PASSED                                       [ 15%]
tests/grph_test.py::FLAKE8 PASSED                                     [ 21%]
tests/grph_test.py::mypy PASSED                                       [ 26%]
tests/grph_test.py::test_exists PASSED                                [ 31%]
tests/grph_test.py::test_usage PASSED                                 [ 36%]
tests/grph_test.py::test_bad_k PASSED                                 [ 42%]
tests/grph_test.py::test_bad_file PASSED                              [ 47%]
tests/grph_test.py::test_01 PASSED                                    [ 52%]
tests/grph_test.py::test_02 PASSED                                    [ 57%]
tests/grph_test.py::test_03 PASSED                                    [ 63%]
tests/grph_test.py::test_04 PASSED                                    [ 68%]
tests/grph_test.py::test_05 PASSED                                    [ 73%]
tests/grph_test.py::test_06 PASSED                                    [ 78%]
tests/grph_test.py::test_07 PASSED                                    [ 84%]
tests/grph_test.py::test_08 PASSED                                    [ 89%]
tests/grph_test.py::test_09 PASSED                                    [ 94%]
::mypy PASSED                                                         [100%]
=================================== mypy ====================================

Success: no issues found in 2 source files
============================ 19 passed in 4.13s =============================

Author

Ken Youens-Clark [email protected]