def test_parse_base_multiplets_basic(self):
"""parse_base_multiplets: basic input"""
basic_lines =\
['235_237_254_| [20 3] 0: 246 G + 0: 248 A + 0: 265 U',\
'273_274_356_| [21 3] 0: 284 C + 0: 285 A + 0: 367 G']
bm1 = BaseMultiplet([Base('0','246','G','235'),\
Base('0','248','A','237'), Base('0','265','U','254')])
bm2 = BaseMultiplet([Base('0','284','C','273'),\
Base('0','285','A','274'), Base('0','367','G','356')])
bms = BaseMultiplets([bm1, bm2])
obs = parse_base_multiplets(basic_lines)
for o, e in zip(obs, bms):
for base_x, base_y in zip(o, e):
self.assertEqual(base_x, base_y)
self.assertEqual(len(obs), 2)
self.assertEqual(len(obs[0]), 3)
basic_lines =\
['235_237_254_| [20 3] 0: 246 G + 0: 248 A + 0: 265 I',\
'273_274_356_| [21 3] 0: 284 P + 0: 285 a + 0: 367 G']
bm1 = BaseMultiplet([Base('0','246','G','235'),\
Base('0','248','A','237'), Base('0','265','I','254')])
bm2 = BaseMultiplet([Base('0','284','P','273'),\
Base('0','285','a','274'), Base('0','367','G','356')])
bms = BaseMultiplets([bm1, bm2])
obs = parse_base_multiplets(basic_lines)
for o, e in zip(obs, bms):
for base_x, base_y in zip(o, e):
self.assertEqual(base_x, base_y)
self.assertEqual(len(obs), 2)
self.assertEqual(len(obs[0]), 3)
def test_init(self):
"""BaseMultiplets __init__: from list and tuple"""
b1 = Base('A', '30', 'A')
b2 = Base('A', '35', 'G')
b3 = Base('A', '360', 'U')
bm1 = BaseMultiplet([b1, b2, b3])
b4 = Base('B', '12', 'C')
b5 = Base('B', '42', 'U')
b6 = Base('C', '2', 'A')
bm2 = BaseMultiplet([b4, b5, b6])
bms = BaseMultiplets([bm1, bm2])
self.assertTrue(bms[0] is bm1)
self.assertTrue(bms[1] is bm2)
self.assertEqual(bms[1][2].ResId, '2')
#should work from tuple also
bms = BaseMultiplets((bm1, bm2))
self.assertTrue(bms[0] is bm1)
self.assertTrue(bms[1] is bm2)
self.assertEqual(bms[1][2].ResId, '2')
def test_str(self):
"""BaseMultiplets __str__: should give expected string"""
b1 = Base('A', '30', 'A')
b2 = Base('A', '35', 'G')
b3 = Base('A', '360', 'U')
bm1 = BaseMultiplet([b1, b2, b3])
b4 = Base('B', '12', 'C')
b5 = Base('B', '42', 'U')
b6 = Base('C', '2', 'A')
bm2 = BaseMultiplet([b4, b5, b6])
bms = BaseMultiplets([bm1, bm2])
exp_lines = [\
"A 30 A -- A 35 G -- A 360 U;",\
"B 12 C -- B 42 U -- C 2 A;"]
self.assertEqual(str(bms), '\n'.join(exp_lines))
def test_RnaviewParser(self):
"""RnaviewParser: should work with/without model and/or verification
"""
rnaview_lines = RNAVIEW_PDB_REAL.split('\n')
obs = RnaviewParser(rnaview_lines)
self.assertEqual(obs['FN'], 'pdb430d.ent')
self.assertEqual(len(obs['UC']), 1)
self.assertEqual(len(obs['BP']), 19)
self.assertEqual(len(obs['BM']), 0)
self.assertEqual(obs['BM'], BaseMultiplets())
self.assertEqual(obs['PC']['Standard'], 7)
self.assertEqual(obs['BP'][2].Down.ResName, 'c')
self.assertEqual(obs['BP'][6].Edges, 'stacked')
self.assertEqual(obs['NP']['NUM_PAIRS'], 11)
self.assertEqual(obs['NP']['NUM_BASES'], 29)