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 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 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_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
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
class SequenceEmbedderTests(TestCase):
"""Tests of the SequenceEmbedder class."""
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_composition_change(self):
"""Changes in composition should propagate."""
rr = str(self.ile_embedder.RandomRegion.Current)
#for base in 'UCAG':
# assert base in rr
#the above two lines should generally be true but fail stochastically
self.ile_embedder.Composition = BaseFrequency('CG')
self.assertEqual(self.ile_embedder.Model.Composition, \
BaseFrequency('CG'))
self.assertEqual(self.ile_embedder.RandomRegion.Composition, \
BaseFrequency('CG'))
self.ile_embedder.RandomRegion.refresh()
self.assertEqual(len(self.ile_embedder.RandomRegion), 22)
rr = str(self.ile_embedder.RandomRegion.Current)
assert ('C' in rr or 'G' in rr)
assert 'A' not in rr
assert 'U' not in rr
def test_choose_locations_too_short(self):
"""SequenceEmbedder _choose_locations should fail if too little space"""
self.ile_embedder.Length = 28 #no positions left over
self.assertRaises(ValueError, self.ile_embedder._choose_locations)
self.ile_embedder.Length = 29 #one position left over
self.assertRaises(ValueError, self.ile_embedder._choose_locations)
def test_choose_locations_exact(self):
"""SequenceEmbedder _choose_locations should pick all locations"""
self.ile_embedder.Length = 30 #two positions left: must both be filled
for i in range(10):
first, second = self.ile_embedder._choose_locations()
self.assertEqual(first, 0)
self.assertEqual(second, 1)
def test_choose_locations_even(self):
"""SequenceEmbedder _choose_locations should pick locations evenly"""
self.ile_embedder.Length = 31 #three positions left
counts = {}
for i in range(1000):
key = tuple(self.ile_embedder._choose_locations())
assert key[0] != key[1]
curr = counts.get(key, 0)
counts[key] = curr + 1
expected = [333, 333, 333]
observed = [counts[(0,1)], counts[(0,2)], counts[(1,2)]]
self.assertSimilarFreqs(observed, expected)
#make sure nothing else snuck in there
self.assertEqual(counts[(0,1)]+counts[(0,2)]+counts[(1,2)], 1000)
def test_choose_locations_with_replacement(self):
"""SequenceEmbedder _choose_locations can sample with replacement"""
self.ile_embedder.Length = 28 #exact fit
self.ile_embedder.WithReplacement = True
for i in range(10):
first, second = self.ile_embedder._choose_locations()
self.assertEqual(first, 0)
self.assertEqual(second, 0)
self.ile_embedder.Length = 29 #one left over: can be 0,0 0,1 1,1
counts = {}
for i in range(1000):
key = tuple(self.ile_embedder._choose_locations())
curr = counts.get(key, 0)
counts[key] = curr + 1
expected = [250, 500, 250]
observed = [counts[(0,0)], counts[(0,1)], counts[(1,1)]]
self.assertSimilarFreqs(observed, expected)
#make sure nothing else snuck in there
self.assertEqual(counts[(0,0)]+counts[(0,1)]+counts[(1,1)], 1000)
def test_insert_modules(self):
"""SequenceEmbedder _insert_modules should make correct sequence"""
ile = self.ile_embedder
ile.Length = 50
ile.RandomRegion.Current[:] = ['A'] * 22
modules = list(ile.Model)
ile.Positions = [0, 0] #try inserting at first position
self.assertEqual(str(ile), modules[0] + modules[1] + 'A'*22)
ile.Positions = [3, 20]
self.assertEqual(str(ile), 'A'*3+modules[0]+'A'*17+modules[1]+'A'*2)
def test_refresh(self):
"""SequenceEmbedder refresh should change module sequences"""
modules_before = list(self.ile_embedder.Model)
random_before = str(self.ile_embedder.RandomRegion.Current)
self.ile_embedder.refresh()
random_after = str(self.ile_embedder.RandomRegion.Current)
self.assertNotEqual(random_before, random_after)
modules_after = list(self.ile_embedder.Model)
for before, after in zip(modules_before, modules_after):
self.assertNotEqual(before, after)
#check that it works twice
self.ile_embedder.refresh()
random_third = str(self.ile_embedder.RandomRegion.Current)
modules_third = list(self.ile_embedder.Model)
self.assertNotEqual(random_third, random_before)
self.assertNotEqual(random_third, random_after)
for first, second, third in \
zip(modules_before, modules_after, modules_third):
self.assertNotEqual(first, third)
self.assertNotEqual(second, third)
def test_countMatches(self):
"""Shouldn't find any Ile matches if all the pairs are GU"""
if not RNAFOLD_PRESENT:
return
self.ile_embedder.NumToDo = 100
self.ile_embedder.Composition = BaseFrequency('GGGGGGGGGU')
self.ile_embedder.Length = 40
good_count = self.ile_embedder.countMatches()
self.assertEqual(good_count, 0)
def test_countMatches_pass(self):
"""Should find some matches against a random background"""
if not RNAFOLD_PRESENT:
return
self.ile_embedder.NumToDo = 100
self.ile_embedder.Composition = BaseFrequency('UCAG')
self.ile_embedder.Length = 40
good_count = self.ile_embedder.countMatches()
self.assertNotEqual(good_count, 0)
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
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 xxx_test_count_long(self):
self.ile_embedder.NumToDo = 100000
self.ile_embedder.Composition = BaseFrequency('UCAG')
print
print "Extended helices"
for length in range(30, 150):
self.ile_embedder.Length = length
good_count = self.ile_embedder.countMatches()
print "Length: %s Matches: %s/100000" % (length, good_count)
print
def xxx_test_count_short(self):
self.short_ile_embedder.NumToDo = 10000
self.short_ile_embedder.Composition = BaseFrequency('UCAG')
print
print "Minimal motif"
for length in range(20, 150):
self.short_ile_embedder.Length = length
good_count = self.short_ile_embedder.countMatches()
print "Length: %s Matches: %s/10000" % (length, good_count)
print