testdriver

#!/usr/bin/env python

import unittest
from align_sequences import smith_waterman

class TestAlignmentMethods(unittest.TestCase):

    # A string aligned to itself should only have matches
    def test_smith_waterman_self(self):
        seq1 = "ACGTTA"
        seq2 = "ACGTTA"
        self.assertEqual(smith_waterman(seq1, seq2, 1, 1, 1, 0),(6, 'ACGTTA','ACGTTA'))

    # A test case with just one mismatch
    def test_smith_waterman_mismatch(self):
        seq1 = "ACGTTA"
        seq2 = "ACCTTA"
        self.assertEqual(smith_waterman(seq1, seq2, 1, 1, 1, 0),(4, 'ACGTTA','ACCTTA'))

    # A test case with one gap in seq2 using a linear gap penalty
    def test_smith_waterman_gap1(self):
        seq1 = "ACGTTA"
        seq2 = "ACTTA"
        self.assertEqual(smith_waterman(seq1, seq2, 1, 1, 1, 0),(4, 'ACGTTA','AC-TTA'))

    # A test case with one gap in seq1 using a linear penalty
    def test_smith_waterman_gap2(self):
        seq1 = "ACTTA"
        seq2 = "ACGTTA"
        self.assertEqual(smith_waterman(seq1, seq2, 1, 1, 1, 0),(4, 'AC-TTA','ACGTTA'))

    # A test case with one gap in seq2 using a affine gap penalty
    def test_smith_waterman_gap1_affine(self):
        seq1 = "ACGTTA"
        seq2 = "ACTA"
        self.assertEqual(smith_waterman(seq1, seq2, 1, 1, 1, 0.5),(2.0, 'ACGTTA','AC--TA'))

    # A test case with one gap in seq1 using a affine gap penalty
    def test_smith_waterman_gap2_affine(self):
        seq1 = "ACTA"
        seq2 = "ACGTTA"
        self.assertIn(smith_waterman(seq1, seq2, 1, 1, 1, 0.5),[(2.0, 'AC--TA','ACGTTA'), (2.0, 'TA', 'TA')]) 

    # A test case with local alignment (alignment does not extend all the way)
    def test_smith_waterman_local(self):
        seq1 = "ACTCGCAATATGCTAGGCCAGC"
        seq2 = "GGTTATGCTATGCGG"
        self.assertEqual(smith_waterman(seq1, seq2, 2, 1, 4, 1),(17, 'TATGCTAGGC','TATGCTATGC'))


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