import csb.test as test from csb.bio.sequence import RichSequence, SequenceTypes from csb.bio.sequence.alignment import IdentityMatrix, SimilarityMatrix from csb.bio.sequence.alignment import GlobalAlignmentAlgorithm, LocalAlignmentAlgorithm, AlignmentResult @test.unit class TestIdentityMatrix(test.Case): def setUp(self): super(TestIdentityMatrix, self).setUp() self.matrix = IdentityMatrix(2, -3) def testScore(self): self.assertEqual(self.matrix.score("a", "a"), 2) self.assertEqual(self.matrix.score("a", "b"), -3) @test.unit class TestSimilarityMatrix(test.Case): def setUp(self): super(TestSimilarityMatrix, self).setUp() self.matrix = SimilarityMatrix(SimilarityMatrix.BLOSUM62) def testScore(self): self.assertEqual(self.matrix.score("A", "A"), 4) self.assertEqual(self.matrix.score("A", "R"), -1) self.assertEqual(self.matrix.score("R", "A"), -1) @test.unit class TestGlobalAlignmentAlgorithm(test.Case): def setUp(self): super(TestGlobalAlignmentAlgorithm, self).setUp() self.seq1 = RichSequence('s1', '', 'CCABBBCBBCABAABCCEAAAAAAAAAAAAFAA', SequenceTypes.Protein) self.seq2 = RichSequence('s1', '', 'AZCBBABAABCCEF', SequenceTypes.Protein) self.algorithm = GlobalAlignmentAlgorithm(scoring=IdentityMatrix(1, -1), gap=0) def testAlign(self): ali = self.algorithm.align(self.seq1, self.seq2) self.assertEqual(ali.query.sequence, "CCA-BBBCBBCABAABCCEAAAAAAAAAAAAFAA") self.assertEqual(ali.subject.sequence, "--AZ---CBB-ABAABCCE------------F--") self.assertEqual(ali.query.residues[3], self.seq1.residues[3]) self.assertTrue(ali.query.residues[3] is self.seq1.residues[3]) self.assertEqual(ali.qstart, 1) self.assertEqual(ali.qend, 33) self.assertEqual(ali.start, 1) self.assertEqual(ali.end, 14) self.assertEqual(ali.length, 34) self.assertEqual(ali.gaps, 21) self.assertEqual(ali.identicals, 13) self.assertEqual(ali.identity, 13 / 34.0 ) self.assertEqual(ali.score, 13) def testEmptyAlignment(self): seq1 = RichSequence('s1', '', 'AAAA', SequenceTypes.Protein) seq2 = RichSequence('s2', '', 'BBBB', SequenceTypes.Protein) ali = self.algorithm.align(seq1, seq2) self.assertTrue(ali.is_empty) @test.unit class TestLocalAlignmentAlgorithm(test.Case): def setUp(self): super(TestLocalAlignmentAlgorithm, self).setUp() self.seq1 = RichSequence('s1', '', 'CCABBBCBBCABAABCCEAAAAAAAAAAAAFAA', SequenceTypes.Protein) self.seq2 = RichSequence('s1', '', 'AZCBBABAACBCCEF', SequenceTypes.Protein) self.algorithm = LocalAlignmentAlgorithm(scoring=IdentityMatrix(1, -1), gap=-1) def testAlign(self): ali = self.algorithm.align(self.seq1, self.seq2) self.assertEqual(ali.query.sequence, "CBBCABAA-BCCE") self.assertEqual(ali.subject.sequence, "CBB-ABAACBCCE") self.assertEqual(ali.qstart, 7) self.assertEqual(ali.qend, 18) self.assertEqual(ali.start, 3) self.assertEqual(ali.end, 14) self.assertEqual(ali.length, 13) self.assertEqual(ali.gaps, 2) self.assertEqual(ali.identicals, 11) self.assertEqual(ali.identity, 11 / 13.0 ) self.assertEqual(ali.score, 9) def testEmptyAlignment(self): seq1 = RichSequence('s1', '', 'AAAA', SequenceTypes.Protein) seq2 = RichSequence('s2', '', 'BBBB', SequenceTypes.Protein) ali = self.algorithm.align(seq1, seq2) self.assertTrue(ali.is_empty) @test.unit class TestAlignmentResult(test.Case): def setUp(self): super(TestAlignmentResult, self).setUp() self.seq1 = RichSequence('s1', '', 'AB-D', SequenceTypes.Protein) self.seq2 = RichSequence('s2', '', 'A-CD', SequenceTypes.Protein) self.ali = AlignmentResult(5.5, self.seq1, self.seq2, 10, 12, 20, 22) self.es = RichSequence('s1', '', '') self.empty = AlignmentResult(0, self.es, self.es, 0, 0, 0, 0) def testConstructor(self): self.assertRaises(ValueError, AlignmentResult, 1, self.es, self.es, 0, 0, 0, 0) self.assertRaises(ValueError, AlignmentResult, 0, self.es, self.es, 1, 0, 0, 0) self.assertRaises(ValueError, AlignmentResult, 0, self.es, self.es, 0, 1, 0, 0) self.assertRaises(ValueError, AlignmentResult, 0, self.es, self.es, 0, 0, 1, 0) self.assertRaises(ValueError, AlignmentResult, 0, self.es, self.es, 0, 0, 0, 1) self.assertRaises(ValueError, AlignmentResult, 1, self.seq1, self.seq2, 0, 0, 0, 0) def testStr(self): string = r""" 10 AB-D 12 20 A-CD 22 """.strip("\r\n") self.assertEqual(string, str(self.ali)) def testAlignment(self): ali = self.ali.alignment() self.assertEqual(ali.rows[1].sequence, self.seq1.sequence) self.assertEqual(ali.rows[2].sequence, self.seq2.sequence) def testQuery(self): self.assertEqual(self.ali.query.sequence, self.seq1.sequence) self.assertEqual(self.ali.query.residues[2], self.seq1.residues[2]) self.assertTrue(self.ali.query.residues[2] is self.seq1.residues[2]) def testSubject(self): self.assertEqual(self.ali.subject.sequence, self.seq2.sequence) self.assertEqual(self.ali.subject.residues[3], self.seq2.residues[3]) self.assertTrue(self.ali.subject.residues[3] is self.seq2.residues[3]) def testQstart(self): self.assertEqual(self.ali.qstart, 10) def testQend(self): self.assertEqual(self.ali.qend, 12) def testStart(self): self.assertEqual(self.ali.start, 20) def testEnd(self): self.assertEqual(self.ali.end, 22) def testLength(self): self.assertEqual(self.ali.length, 4) def testScore(self): self.assertEqual(self.ali.score, 5.5) def testGaps(self): self.assertEqual(self.ali.gaps, 2) def testIdenticals(self): self.assertEqual(self.ali.identicals, 2) def testIdentity(self): self.assertEqual(self.ali.identity, 0.5) def testIsEmpty(self): self.assertFalse(self.ali.is_empty) es = RichSequence('s1', '', '') empty = AlignmentResult(0, es, es, 0, 0, 0, 0) self.assertTrue(empty.is_empty) if __name__ == '__main__': test.Console()