test_sequence_alignment.py

from abc import ABC, abstractmethod
import unittest
from sequence_alignment import GlobalAlignment, LocalAlignment


class TestCase:
   def __init__(self, input_seq, expected_global_output, expected_local_output):
       self.input_seq = input_seq
       self.expected_global_output = expected_global_output
       self.expected_local_output = expected_local_output

#############################

class TestAlignment(ABC, unittest.TestCase):
    SAME_LENGTH_SEQ_CASES = [
        TestCase(('TGGTG', 'ATCGT'), ('-TGGTG', 'ATCGT-'), ('GT', 'GT')),
        TestCase(('TCGTAGG', 'CTCGTAT'), ('-TCGTAGG', 'CTCGTAT-'), ('TCGTA', 'TCGTA')),
        TestCase(('ATCGT', 'GTCGA'), ('ATCGT', 'GTCGA'), ('TCG', 'TCG'))
    ]

    DIFF_LENGTH_SEQ_CASES = [
        TestCase(('ATCGT', 'AT'), ('ATCGT', 'AT---'), ('AT', 'AT')),
        TestCase(('ATCGTATCGT', 'CGA'), ('ATCGTATCGT', '--CG-A----'), ('CG', 'CG')),
        TestCase(('ATCGT', 'TCG'), ('ATCGT', '-TCG-'), ('TCG', 'TCG')),
        TestCase(('ATCGTATCGT', 'TCGATCG'), ('ATCGTATCGT', '-TCG-ATCG-'), ('TCGTATCG', 'TCG-ATCG')),
        TestCase(('ATCGTATCGT', 'ATCTTTCGTC'), ('ATCGTATCGT-', 'ATCTT-TCGTC'), ('ATCGTATCGT', 'ATCTT-TCGT')),
        TestCase(('ATCGACC', 'GCATCTA'), ('--ATCGACC', 'GCATCTA--'), ('ATC', 'ATC')),
        TestCase(('ACCTAAGG', 'GGCTCAATCA'), ('ACCT-AAGG-', 'GGCTCAATCA'), ('CT', 'CT'))
    ]

    EMPTY_SEQ_CASES = [
        TestCase(('', 'ATCGT'), ('-----', 'ATCGT'), ('', '')),
        TestCase(('', ''), ('', ''), ('', ''))
    ]

    def run_test_cases(self, test_cases, AlignmentClass):
       for case in test_cases:
           with self.subTest(case=case):
               expected_output = case.expected_global_output if AlignmentClass == GlobalAlignment else case.expected_local_output
               self.assertEqual(AlignmentClass(case.input_seq).align, expected_output)


    @abstractmethod
    def test_same_length_seq(self):
       pass


    @abstractmethod
    def test_diff_length_seq(self):
       pass


    @abstractmethod
    def test_empty_seq(self):
       pass

#############################

# python3 -m unittest -v test_sequence_alignment.TestGlobalAlignment
class TestGlobalAlignment(TestAlignment):
   AlignmentClass = GlobalAlignment

   def test_same_length_seq(self):
       super().run_test_cases(self.SAME_LENGTH_SEQ_CASES, self.AlignmentClass)


   def test_diff_length_seq(self):
       super().run_test_cases(self.DIFF_LENGTH_SEQ_CASES, self.AlignmentClass)


   def test_empty_seq(self):
       super().run_test_cases(self.EMPTY_SEQ_CASES, self.AlignmentClass)

#############################

# python3 -m unittest -v test_sequence_alignment.TestLocalAlignment
class TestLocalAlignment(TestAlignment):
   AlignmentClass = LocalAlignment

   def test_same_length_seq(self):
       super().run_test_cases(self.SAME_LENGTH_SEQ_CASES, self.AlignmentClass)


   def test_diff_length_seq(self):
       super().run_test_cases(self.DIFF_LENGTH_SEQ_CASES, self.AlignmentClass)


   def test_empty_seq(self):
       super().run_test_cases(self.EMPTY_SEQ_CASES, self.AlignmentClass)

#############################

if __name__ == '__main__':
   unittest.main()