class TestHit(test.Case):
def setUp(self):
super(TestHit, self).setUp()
self.h1 = HHpredHit(1, 'hit1', 2, 5, 3, 6, 0.5, 10)
self.h2 = HHpredHit(2, 'hit2', 3, 5, 4, 6, 0.2, 10)
def testEquals(self):
hit = HHpredHit(1, 'hit1', 2, 5, 3, 6, 0.5, 10)
self.assertTrue(self.h1.equals(hit))
def testSurpasses(self):
self.assertTrue(self.h1.surpasses(HHpredHit(5, 'hitX', 2, 3, 3, 4, 0.5, 10)))
self.assertTrue(self.h1.surpasses(HHpredHit(5, 'hitX', 2, 5, 3, 6, 0.3, 10)))
def testIncludes(self):
self.assertTrue(self.h1.includes(HHpredHit(5, 'hit1', 2, 3, 3, 4, 0.5, 10)))
self.assertTrue(self.h1.includes(HHpredHit(5, 'hit1', 2, 4, 3, 5, 0.3, 10)))
self.assertTrue(self.h1.includes(HHpredHit(5, 'hit1', 2, 8, 3, 9, 0.3, 10), tolerance=3))
self.assertFalse(self.h1.includes(HHpredHit(5, 'hit1', 2, 8, 3, 9, 0.3, 10), tolerance=2))
self.assertTrue(self.h1.includes(HHpredHit(5, 'hit1', 1, 5, 2, 6, 0.3, 10), tolerance=1))
self.assertFalse(self.h1.includes(HHpredHit(5, 'hit1', 1, 5, 2, 6, 0.3, 10), tolerance=0))
def testLength(self):
self.assertEqual(self.h1.length, 4)
def testAlignment(self):
q, s = 'AB-D', 'A-CD'
self.h1.add_alignment(q, s)
# query, subject
self.assertEqual(self.h1.alignment.query, q)
self.assertEqual(self.h1.alignment.subject, s)
# segments
segments = list(self.h1.alignment.segments)
self.assertEqual(len(segments), 2)
self.assertEqual(segments[0].qstart, 3)
self.assertEqual(segments[0].qend, 3)
self.assertEqual(segments[0].start, 2)
self.assertEqual(segments[0].end, 2)
self.assertEqual(segments[1].qstart, 5)
self.assertEqual(segments[1].qend, 5)
self.assertEqual(segments[1].start, 4)
self.assertEqual(segments[1].end, 4)
# to_a3m
a3m = self.h1.alignment.to_a3m().format(headers=False)
self.assertEqual(a3m.strip(), 'ABD\nA-cD')
class TestHit(test.Case):
def setUp(self):
super(TestHit, self).setUp()
self.h1 = HHpredHit(1, 'hit1', 2, 5, 3, 6, 0.5, 10)
self.h2 = HHpredHit(2, 'hit2', 3, 5, 4, 6, 0.2, 10)
def testEquals(self):
hit = HHpredHit(1, 'hit1', 2, 5, 3, 6, 0.5, 10)
self.assertTrue(self.h1.equals(hit))
def testSurpasses(self):
self.assertTrue(
self.h1.surpasses(HHpredHit(5, 'hitX', 2, 3, 3, 4, 0.5, 10)))
self.assertTrue(
self.h1.surpasses(HHpredHit(5, 'hitX', 2, 5, 3, 6, 0.3, 10)))
def testIncludes(self):
self.assertTrue(
self.h1.includes(HHpredHit(5, 'hit1', 2, 3, 3, 4, 0.5, 10)))
self.assertTrue(
self.h1.includes(HHpredHit(5, 'hit1', 2, 4, 3, 5, 0.3, 10)))
self.assertTrue(
self.h1.includes(HHpredHit(5, 'hit1', 2, 8, 3, 9, 0.3, 10),
tolerance=3))
self.assertFalse(
self.h1.includes(HHpredHit(5, 'hit1', 2, 8, 3, 9, 0.3, 10),
tolerance=2))
self.assertTrue(
self.h1.includes(HHpredHit(5, 'hit1', 1, 5, 2, 6, 0.3, 10),
tolerance=1))
self.assertFalse(
self.h1.includes(HHpredHit(5, 'hit1', 1, 5, 2, 6, 0.3, 10),
tolerance=0))
def testLength(self):
self.assertEqual(self.h1.length, 4)
def testAlignment(self):
q, s = 'AB-D', 'A-CD'
self.h1.add_alignment(q, s)
# query, subject
self.assertEqual(self.h1.alignment.query, q)
self.assertEqual(self.h1.alignment.subject, s)
# segments
segments = list(self.h1.alignment.segments)
self.assertEqual(len(segments), 2)
self.assertEqual(segments[0].qstart, 3)
self.assertEqual(segments[0].qend, 3)
self.assertEqual(segments[0].start, 2)
self.assertEqual(segments[0].end, 2)
self.assertEqual(segments[1].qstart, 5)
self.assertEqual(segments[1].qend, 5)
self.assertEqual(segments[1].start, 4)
self.assertEqual(segments[1].end, 4)
# to_a3m
a3m = self.h1.alignment.to_a3m().format(headers=False)
self.assertEqual(a3m.strip(), 'ABD\nA-cD')
