/usr/lib/python2.7/dist-packages/csb/test/cases/bio/sequence/alignment/__init__.py is in python-csb 1.2.3+dfsg-3.
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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()
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