def test_PresentChains(self):
"""BasePairs PresentChains: should work on single/multiple chain(s)"""
bps = BasePairs([self.a1, self.a2, self.a3, self.a4])
self.assertEqual(bps.PresentChains, ['A'])
bps = BasePairs([self.a1, self.ab1])
self.assertEqualItems(bps.PresentChains, ['A', 'B'])
bps = BasePairs([self.a1, self.ab1, self.ac1, self.bc1])
self.assertEqualItems(bps.PresentChains, ['A', 'B', 'C'])
bps = BasePairs([self.a1, self.ab1, self.bn1])
self.assertEqualItems(bps.PresentChains, [None, 'A', 'B'])
def test_hasConflicts(self):
"""BasePairs hadConflicts: handle chains and residue IDs"""
# no conflict
b1 = BasePair(Base("A", "30", "G"), Base("A", "36", "C"), Saenger="XX")
b2 = BasePair(Base("A", "31", "A"), Base("A", "35", "U"), Orientation="cis", Edges="W/W")
b3 = BasePair(Base("A", "15", "G"), Base("A", "42", "C"))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(), False)
self.assertEqual(bps.hasConflicts(return_conflict=True), (False, None))
# conflict within chain
b1 = BasePair(Base("A", "30", "G"), Base("A", "36", "C"), Saenger="XX")
b2 = BasePair(Base("A", "31", "A"), Base("A", "35", "U"), Orientation="cis", Edges="W/W")
b3 = BasePair(Base("A", "30", "G"), Base("A", "42", "C"))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(), True)
# conflict within chain -- return conflict
b1 = BasePair(Base("A", "30", "G"), Base("A", "36", "C"), Saenger="XX")
b2 = BasePair(Base("A", "31", "A"), Base("A", "35", "U"), Orientation="cis", Edges="W/W")
b3 = BasePair(Base("A", "30", "G"), Base("A", "42", "C"))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(return_conflict=True), (True, "A 30 G"))
# no conflict, same residue ID, different chain
b1 = BasePair(Base("A", "30", "G"), Base("A", "36", "C"), Saenger="XX")
b2 = BasePair(Base("A", "31", "A"), Base("A", "35", "U"), Orientation="cis", Edges="W/W")
b3 = BasePair(Base("C", "30", "G"), Base("A", "42", "C"))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(), False)
def test_hasConflicts(self):
"""BasePairs hadConflicts: handle chains and residue IDs"""
# no conflict
b1 = BasePair(Base('A','30','G'), Base('A','36','C'), Saenger='XX')
b2 = BasePair(Base('A','31','A'), Base('A','35','U'),\
Orientation='cis',Edges='W/W')
b3 = BasePair(Base('A','15','G'), Base('A','42','C'))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(), False)
self.assertEqual(bps.hasConflicts(return_conflict=True), (False, None))
# conflict within chain
b1 = BasePair(Base('A','30','G'), Base('A','36','C'), Saenger='XX')
b2 = BasePair(Base('A','31','A'), Base('A','35','U'),\
Orientation='cis',Edges='W/W')
b3 = BasePair(Base('A','30','G'), Base('A','42','C'))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(), True)
# conflict within chain -- return conflict
b1 = BasePair(Base('A','30','G'), Base('A','36','C'), Saenger='XX')
b2 = BasePair(Base('A','31','A'), Base('A','35','U'),\
Orientation='cis',Edges='W/W')
b3 = BasePair(Base('A','30','G'), Base('A','42','C'))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(return_conflict=True),\
(True, "A 30 G"))
# no conflict, same residue ID, different chain
b1 = BasePair(Base('A','30','G'), Base('A','36','C'), Saenger='XX')
b2 = BasePair(Base('A','31','A'), Base('A','35','U'),\
Orientation='cis',Edges='W/W')
b3 = BasePair(Base('C','30','G'), Base('A','42','C'))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(), False)
def test_init(self):
"""BasePairs __init__: should work with or without Model"""
# init from list
bps = BasePairs([self.a1, self.a2])
self.assertTrue(bps[0] is self.a1)
self.assertTrue(bps[1] is self.a2)
# init from tuple
bps = BasePairs((self.a1, self.a2))
self.assertTrue(bps[0] is self.a1)
self.assertTrue(bps[1] is self.a2)
def test_parse_base_pairs_basic(self):
"""parse_base_pairs: basic input"""
basic_lines =\
['25_437, 0: 34 C-G 448 0: +/+ cis XIX',\
'26_436, 0: 35 U-A 447 0: -/- cis XX']
bp1 = BasePair(Up=Base('0','34','C','25'),\
Down=Base('0','448','G','437'),\
Edges='+/+', Orientation='cis',Conformation=None,Saenger='XIX')
bp2 = BasePair(Up=Base('0','35','U','26'),\
Down=Base('0','447','A','436'),\
Edges='-/-', Orientation='cis',Conformation=None,Saenger='XX')
bps = BasePairs([bp1, bp2])
obs = parse_base_pairs(basic_lines)
for o, e in zip(obs, [bp1, bp2]):
self.assertEqual(o, e)
self.assertEqual(len(obs), 2)
basic_lines =\
['25_437, 0: 34 c-P 448 0: +/+ cis XIX',\
'26_436, 0: 35 U-X 447 0: -/- cis XX']
self.assertRaises(RnaViewParseError, parse_base_pairs, basic_lines)
basic_lines =\
['25_437, 0: 34 c-P 448 0: +/+ cis XIX',\
'26_436, 0: 35 I-A 447 0: -/- cis XX']
bp1 = BasePair(Up=Base('0','34','c','25'),\
Down=Base('0','448','P','437'),\
Edges='+/+', Orientation='cis',Conformation=None,Saenger='XIX')
bp2 = BasePair(Up=Base('0','35','I','26'),\
Down=Base('0','447','A','436'),\
Edges='-/-', Orientation='cis',Conformation=None,Saenger='XX')
bps = BasePairs([bp1, bp2])
obs = parse_base_pairs(basic_lines)
for o, e in zip(obs, [bp1, bp2]):
self.assertEqual(o, e)
self.assertEqual(len(obs), 2)
lines = ['1_2, : 6 G-G 7 : stacked',\
'1_16, : 6 G-C 35 : +/+ cis XIX']
bp1 = BasePair(Up=Base(' ','6','G','1'),\
Down=Base(' ','7','G','2'), Edges='stacked')
bp2 = BasePair(Up=Base(' ','6','G','1'),\
Down=Base(' ','35','C','16'),\
Edges='+/+', Orientation='cis',Conformation=None,Saenger='XIX')
obs = parse_base_pairs(lines)
for o, e in zip(obs, [bp1, bp2]):
self.assertEqual(o, e)
self.assertEqual(len(obs), 2)
def test_select(self):
"""BasePairs select: should work with any good function"""
def xx(bp):
if bp.Saenger == 'XX':
return True
return False
bps = BasePairs([self.a1, self.a2, self.a3, self.a4])
obs = bps.select(xx)
self.assertEqual(len(obs), 2)
self.assertTrue(obs[0] is self.a1)
self.assertTrue(obs[1] is self.a2)
for i in obs:
self.assertEqual(i.Saenger, 'XX')
def test_select(self):
"""BasePairs select: should work with any good function"""
def xx(bp):
if bp.Saenger == "XX":
return True
return False
bps = BasePairs([self.a1, self.a2, self.a3, self.a4])
obs = bps.select(xx)
self.assertEqual(len(obs), 2)
self.failUnless(obs[0] is self.a1)
self.failUnless(obs[1] is self.a2)
for i in obs:
self.assertEqual(i.Saenger, "XX")
def setUp(self):
"""setUp method for all BasePairs tests"""
self.a1 = BasePair(Base('A', '30', 'G'),
Base('A', '36', 'C'),
Saenger='XX')
self.a2 = BasePair(Base('A', '31', 'A'),
Base('A', '35', 'U'),
Saenger='XX')
self.a3 = BasePair(Base('A', '40', 'G'),
Base('A', '60', 'U'),
Saenger='V')
self.a4 = BasePair(Base('A','41','A'), Base('A','58','U'),\
Saenger=None)
self.ab1 = BasePair(Base('A', '41', 'A'), Base('B', '58', 'U'))
self.ac1 = BasePair(Base('A', '10', 'C'), Base('C', '3', 'G'))
self.bc1 = BasePair(Base('B', '41', 'A'), Base('C', '1', 'U'))
self.bn1 = BasePair(Base('B', '41', 'A'), Base(None, '1', 'U'))
self.cd1 = BasePair(Base('C', '41', 'A'), Base('D', '1', 'U'))
self.bp1 = BasePair(Base('A', '34', 'U'), Base('A', '40', 'A'))
self.bp2 = BasePair(Base('A', '35', 'C'), Base('A', '39', 'G'))
self.bp3 = BasePair(Base('B', '32', 'G'), Base('B', '38', 'U'))
self.bp4 = BasePair(Base('B', '33', 'G'), Base('B', '37', 'C'))
self.bp5 = BasePair(Base('A', '31', 'C'), Base('B', '41', 'G'))
self.bp6 = BasePair(Base('A', '32', 'U'), Base('B', '40', 'A'))
self.bp7 = BasePair(Base('A', '37', 'U'), Base('B', '35', 'A'))
self.pairs = BasePairs([self.bp1, self.bp2, self.bp3, self.bp4,\
self.bp5, self.bp6, self.bp7])
def test_str(self):
"""BasePairs __str__: should produce expected string"""
b1 = BasePair(Base('A', '30', 'G'), Base('A', '36', 'C'), Saenger='XX')
b2 = BasePair(Base('A','31','A'), Base('A','35','U'),\
Orientation='cis',Edges='W/W')
bps = BasePairs([b1, b2])
exp_lines = [
"===================================================================",\
"Bases: Up -- Down; Annotation: Edges -- Orient. -- Conf. -- Saenger",\
"===================================================================",\
"Bases: A 30 G -- A 36 C; Annotation: None -- None -- None -- XX;",\
"Bases: A 31 A -- A 35 U; Annotation: W/W -- cis -- None -- None;"]
self.assertEqual(str(bps), '\n'.join(exp_lines))
def test_cliques(self):
"""BasePairs cliques: single/multiple chains and cliques"""
#one chain, one clique
bps = BasePairs([self.a1, self.a2, self.a3, self.a4])
obs_cl = list(bps.cliques())
self.assertEqual(len(obs_cl), 1)
#3 chains, 2 cliques
bps = BasePairs([self.a1, self.a2, self.cd1])
obs_cl = list(bps.cliques())
self.assertEqual(len(obs_cl), 2)
self.assertEqual(len(obs_cl[0]), 2)
self.assertEqual(len(obs_cl[1]), 1)
self.failUnless(obs_cl[1][0] is self.cd1)
self.assertEqual(obs_cl[1].PresentChains, ['C','D'])
#5 chains, 1 clique
bps = BasePairs([self.a1, self.ab1, self.bc1, self.bn1, self.cd1])
obs_cl = list(bps.cliques())
self.assertEqual(len(obs_cl), 1)
self.assertEqual(len(obs_cl[0]), 5)
self.failUnless(obs_cl[0][0] is self.a1)
self.assertEqualItems(obs_cl[0].PresentChains, ['A','B','C','D', None])
def test_cliques(self):
"""BasePairs cliques: single/multiple chains and cliques"""
# one chain, one clique
bps = BasePairs([self.a1, self.a2, self.a3, self.a4])
obs_cl = list(bps.cliques())
self.assertEqual(len(obs_cl), 1)
# 3 chains, 2 cliques
bps = BasePairs([self.a1, self.a2, self.cd1])
obs_cl = list(bps.cliques())
self.assertEqual(len(obs_cl), 2)
self.assertEqual(len(obs_cl[0]), 2)
self.assertEqual(len(obs_cl[1]), 1)
self.failUnless(obs_cl[1][0] is self.cd1)
self.assertEqual(obs_cl[1].PresentChains, ["C", "D"])
# 5 chains, 1 clique
bps = BasePairs([self.a1, self.ab1, self.bc1, self.bn1, self.cd1])
obs_cl = list(bps.cliques())
self.assertEqual(len(obs_cl), 1)
self.assertEqual(len(obs_cl[0]), 5)
self.failUnless(obs_cl[0][0] is self.a1)
self.assertEqualItems(obs_cl[0].PresentChains, ["A", "B", "C", "D", None])
def test_hasConflicts(self):
"""BasePairs hadConflicts: handle chains and residue IDs"""
# no conflict
b1 = BasePair(Base('A', '30', 'G'), Base('A', '36', 'C'), Saenger='XX')
b2 = BasePair(Base('A','31','A'), Base('A','35','U'),\
Orientation='cis',Edges='W/W')
b3 = BasePair(Base('A', '15', 'G'), Base('A', '42', 'C'))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(), False)
self.assertEqual(bps.hasConflicts(return_conflict=True), (False, None))
# conflict within chain
b1 = BasePair(Base('A', '30', 'G'), Base('A', '36', 'C'), Saenger='XX')
b2 = BasePair(Base('A','31','A'), Base('A','35','U'),\
Orientation='cis',Edges='W/W')
b3 = BasePair(Base('A', '30', 'G'), Base('A', '42', 'C'))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(), True)
# conflict within chain -- return conflict
b1 = BasePair(Base('A', '30', 'G'), Base('A', '36', 'C'), Saenger='XX')
b2 = BasePair(Base('A','31','A'), Base('A','35','U'),\
Orientation='cis',Edges='W/W')
b3 = BasePair(Base('A', '30', 'G'), Base('A', '42', 'C'))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(return_conflict=True),\
(True, "A 30 G"))
# no conflict, same residue ID, different chain
b1 = BasePair(Base('A', '30', 'G'), Base('A', '36', 'C'), Saenger='XX')
b2 = BasePair(Base('A','31','A'), Base('A','35','U'),\
Orientation='cis',Edges='W/W')
b3 = BasePair(Base('C', '30', 'G'), Base('A', '42', 'C'))
bps = BasePairs([b1, b2, b3])
self.assertEqual(bps.hasConflicts(), False)
