def setUp(self):
"""Define a few standard models and motifs"""
ile_mod_0 = Module('NNNCUACNNNNN', '(((((..(((((')
ile_mod_1 = Module('NNNNNUAUUGGGGNNN', ')))))......)))))')
ile_rule_0 = Rule(0, 0, 1, 15, 5)
ile_rule_1 = Rule(0, 7, 1, 4, 5)
ile_motif = Motif([ile_mod_0, ile_mod_1], \
[ile_rule_0, ile_rule_1])
helices = [PairedRegion('NNN'), PairedRegion('NNNNN')]
constants = [ConstantRegion('CUAC'), ConstantRegion('UAUUGGGG')]
order = "H0 C0 H1 - H1 C1 H0"
ile_model = SequenceModel(order=order, constants=constants, \
helices=helices, composition=BaseFrequency('UCAG'))
self.ile_embedder = SequenceEmbedder(length=50, num_to_do=10, \
motif=ile_motif, model=ile_model, composition=BaseFrequency('UCAG'))
short_ile_mod_0 = Module('NCUACNN', '(((..((')
short_ile_mod_1 = Module('NNUAUUGGGGN', '))......)))')
short_ile_rule_0 = Rule(0, 0, 1, 10, 3)
short_ile_rule_1 = Rule(0, 5, 1, 1, 2)
short_ile_motif = Motif([short_ile_mod_0, short_ile_mod_1], \
[short_ile_rule_0, short_ile_rule_1])
short_helices = [PairedRegion('N'), PairedRegion('NN')]
short_constants = [ConstantRegion('CUAC'), ConstantRegion('UAUUGGGG')]
short_order = "H0 C0 H1 - H1 C1 H0"
short_ile_model = SequenceModel(order=short_order, \
constants=short_constants, \
helices=short_helices, composition=BaseFrequency('UCAG'))
self.short_ile_embedder = SequenceEmbedder(length=50, num_to_do=10, \
motif=short_ile_motif, model=short_ile_model, \
composition=BaseFrequency('UCAG'))
def test_refresh_primers(self):
"""Module should appear in correct location with primers"""
first_module = Module('AAAAA', '(((((')
second_module = Module('UUUUU', ')))))')
rule_1 = Rule(0, 0, 1, 4, 5)
helix = Motif([first_module, second_module], [rule_1])
model = SequenceModel(constants=[ConstantRegion('AAAAA'), \
ConstantRegion('UUUUU')], order='C0 - C1', \
composition=BaseFrequency('A'))
embedder = SequenceEmbedder(length=30, num_to_do=100, \
motif=helix, model=model, composition=BaseFrequency('CG'), \
positions=[3, 6], primer_5 = 'UUU', primer_3 = 'AAA')
last = ''
for i in range(100):
embedder.refresh()
curr = str(embedder)
self.assertEqual(curr[0:3], 'UUU')
self.assertEqual(curr[6:11], 'AAAAA')
self.assertEqual(curr[14:19], 'UUUUU')
self.assertEqual(curr.count('A'), 8)
self.assertEqual(curr.count('U'), 8)
self.assertEqual(curr[-3:], 'AAA')
self.assertNotEqual(last, curr)
last = curr
def test_init(self):
"""SequenceModel should init OK with Isoleucine motif."""
helices = [PairedRegion('NNN'), PairedRegion('NNNNN')]
constants = [ConstantRegion('CUAC'), ConstantRegion('UAUUGGGG')]
order = "H0 C0 H1 - H1 C1 H0"
isoleucine = SequenceModel(order=order, constants=constants, \
helices=helices)
isoleucine.Composition = BaseFrequency('UCAG')
#print
#print
for i in range(10):
isoleucine.refresh()
#print list(isoleucine)
#print
isoleucine.Composition = BaseFrequency('UCAG')
isoleucine.GU = False
#print
for i in range(10):
isoleucine.refresh()
def test_init(self):
"""SequenceModel should init OK with Isoleucine motif."""
helices = [PairedRegion("NNN"), PairedRegion("NNNNN")]
constants = [ConstantRegion("CUAC"), ConstantRegion("UAUUGGGG")]
order = "H0 C0 H1 - H1 C1 H0"
isoleucine = SequenceModel(order=order, constants=constants, helices=helices)
isoleucine.Composition = BaseFrequency("UCAG")
# print
# print
for i in range(10):
isoleucine.refresh()
# print list(isoleucine)
# print
isoleucine.Composition = BaseFrequency("UCAG")
isoleucine.GU = False
# print
for i in range(10):
isoleucine.refresh()
def test_refresh_specific_position(self):
"""Should always find the module in the same position if specified"""
first_module = Module('AAAAA', '(((((')
second_module = Module('UUUUU', ')))))')
rule_1 = Rule(0, 0, 1, 4, 5)
helix = Motif([first_module, second_module], [rule_1])
model = SequenceModel(constants=[ConstantRegion('AAAAA'), \
ConstantRegion('UUUUU')], order='C0 - C1', \
composition=BaseFrequency('A'))
embedder = SequenceEmbedder(length=30, num_to_do=100, \
motif=helix, model=model, composition=BaseFrequency('CG'), \
positions=[3, 6])
last = ''
for i in range(100):
embedder.refresh()
curr = str(embedder)
self.assertEqual(curr[3:8], 'AAAAA')
self.assertEqual(curr[11:16], 'UUUUU')
self.assertEqual(curr.count('A'), 5)
self.assertEqual(curr.count('U'), 5)
self.assertNotEqual(last, curr)
last = curr