def testOneAlignment(self): """ When one alignment is present that alignment must be returned by bestAlignment. """ alignment = Alignment(44, 'Seq 1') alignment.addHsp(HSP(10)) alignment.addHsp(HSP(9)) alignments = [alignment] hit = ReadAlignments(Read('id1', 'aaa'), alignments) best = bestAlignment(hit) self.assertEqual('Seq 1', best.subjectTitle) self.assertEqual(44, best.subjectLength)
def testOneAlignment(self): """ When one alignment is present that alignment must be returned by bestAlignment. """ alignment = Alignment(44, 'Seq 1') alignment.addHsp(HSP(10)) alignment.addHsp(HSP(9)) alignments = [alignment] hit = ReadAlignments(Read('id1', 'aaa'), alignments) best = bestAlignment(hit) self.assertEqual('Seq 1', best.subjectTitle) self.assertEqual(44, best.subjectLength)
def testThreeAlignments(self): """ When three alignments are present, the one with the highest first HSP must be returned by bestAlignment. """ alignment1 = Alignment(33, 'Seq 1') alignment1.addHsp(HSP(10)) alignment1.addHsp(HSP(9)) alignment2 = Alignment(44, 'Seq 2') alignment2.addHsp(HSP(30)) alignment2.addHsp(HSP(29)) alignment3 = Alignment(55, 'Seq 3') alignment3.addHsp(HSP(20)) alignment3.addHsp(HSP(19)) alignments = [alignment1, alignment2, alignment3] hit = ReadAlignments(Read('id1', 'aaa'), alignments) best = bestAlignment(hit) self.assertEqual('Seq 2', best.subjectTitle) self.assertEqual(44, best.subjectLength)
def testThreeAlignments(self): """ When three alignments are present, the one with the highest first HSP must be returned by bestAlignment. """ alignment1 = Alignment(33, 'Seq 1') alignment1.addHsp(HSP(10)) alignment1.addHsp(HSP(9)) alignment2 = Alignment(44, 'Seq 2') alignment2.addHsp(HSP(30)) alignment2.addHsp(HSP(29)) alignment3 = Alignment(55, 'Seq 3') alignment3.addHsp(HSP(20)) alignment3.addHsp(HSP(19)) alignments = [alignment1, alignment2, alignment3] hit = ReadAlignments(Read('id1', 'aaa'), alignments) best = bestAlignment(hit) self.assertEqual('Seq 2', best.subjectTitle) self.assertEqual(44, best.subjectLength)