def test_ComplexDomains(self):
foo = objects.Complex(sequence=[
self.d1, self.d2, self.d3, '+', self.d1, '+', self.d1c, self.d3c,
self.d1c, self.d2
],
structure=list('..(+(+))..'))
self.assertEqual(foo.sequence, [
self.d1, self.d2, self.d3, '+', self.d1, '+', self.d1c, self.d3c,
self.d1c, self.d2
])
self.assertEqual(foo.lol_sequence,
[[self.d1, self.d2, self.d3], [self.d1],
[self.d1c, self.d3c, self.d1c, self.d2]])
self.assertEqual(foo.nucleotide_sequence,
list('YYYYYNNNNNRRRRR+YYYYY+RRRRRYYYYYRRRRRNNNNN'))
bar = objects.Complex(sequence=[
self.d1c, self.d3c, self.d1c, self.d2, '+', self.d1, self.d2,
self.d3, '+', self.d1
],
structure=list('((..+..)+)'))
self.assertEqual(foo, bar)
self.assertTrue(foo == bar)
def test_IO_kernel(self):
t0 = self.t0
t1 = self.t1
t2 = self.t2
d3 = self.d3
d4 = self.d4
d5 = self.d5
d6 = self.d6
d7 = self.d7
t0c = self.t0c
t1c = self.t1c
t2c = self.t2c
d3c = self.d3c
d4c = self.d4c
d5c = self.d5c
d6c = self.d6c
d7c = self.d7c
sequence = [
d4, t0, '+', d6, t2, '+', d3, '+', d3, t2, '+', t0, d5, t1, '+',
t0, d7, t1, '+', t1c, d7c, t1c, d5c, t2c, '+', d3c, d3c, t2c, d6c,
t0c, d4c, t0c
]
structure = [
'(', '(', '+', '(', '(', '+', '(', '+', '(', '(', '+', '.', '(',
'(', '+', '.', '(', '(', '+', ')', ')', ')', ')', ')', '+', ')',
')', ')', ')', ')', ')', '.'
]
foo = objects.Complex(sequence=sequence, structure=structure)
fooIO = objects.TestTubeIO(
objects.TestTube(complexes={foo.name: (foo, float("inf"), None)}))
f = open(os.devnull, "w")
fooIO.write_pil_kernel(f)
def test_ComplexInit(self):
#NOTE: There is no particular reason for this Error, so it might change!
with self.assertRaises(objects.NuskellObjectError):
foo = objects.Complex()
foo = objects.Complex(sequence=list('RNNNY'), structure=list('(...)'))
self.assertIsInstance(foo, objects.Complex)
self.assertEqual(foo.sequence, list('RNNNY'))
self.assertEqual(foo.structure, list('(...)'))
self.assertEqual(foo.lol_sequence, [list('RNNNY')])
self.assertEqual(foo.nucleotide_sequence, list('RNNNY'))
self.assertEqual(foo.rotate_once, foo)
for r in foo.rotate:
self.assertEqual(r.sequence, list('RNNNY'))
self.assertEqual(r.structure, list('(...)'))
def _TestTube_from_DOM(self, domstring):
solution = objects.TestTube()
[doms, cplxs] = np.parse_dom_string(domstring)
domains = dict()
for n, l in doms:
domains[n] = objects.Domain(list('N'*int(l)), name=n)
domains[n+'*'] = domains[n].get_ComplementDomain(list('N'*int(l)))
for n, se, ss in cplxs:
for e, x in enumerate(se) :
x = ''.join(x)
if x == '+' : continue
se[e] = domains[x]
cx = objects.Complex(se, ss, name=n)
solution.add_complex(cx, (float('inf'), True))
return solution
def test_names(self):
objects.reset_names()
foo = objects.Complex(sequence=[
self.d1, self.d2, self.d3, '+', self.d1, '+', self.d1c, self.d3c,
self.d1c, self.d2
],
structure=list('..(+(+))..'))
self.assertEqual(foo.name, 'cplx0')
with self.assertRaises(objects.NuskellObjectError):
foo.name = 'bar'
objects.reset_names()
foo.name = 'foo'
self.assertEqual(foo.name, 'foo')
self.assertSetEqual(objects.Complex.names, set(['foo']))
foo.name = 'bar'
self.assertEqual(foo.name, 'bar')
self.assertSetEqual(objects.Complex.names, set(['bar']))
objects.reset_names()
def test_IO_dna(self):
# NOTE: This function writes to a file, so we need to compare it to
# pre-written output-file. Doesn't feel necessary at this point ...
t0 = self.t0
t1 = self.t1
t2 = self.t2
d3 = self.d3
d4 = self.d4
d5 = self.d5
d6 = self.d6
d7 = self.d7
t0c = self.t0c
t1c = self.t1c
t2c = self.t2c
d3c = self.d3c
d4c = self.d4c
d5c = self.d5c
d6c = self.d6c
d7c = self.d7c
sequence = [
d4, t0, '+', d6, t2, '+', d3, '+', d3, t2, '+', t0, d5, t1, '+',
t0, d7, t1, '+', t1c, d7c, t1c, d5c, t2c, '+', d3c, d3c, t2c, d6c,
t0c, d4c, t0c
]
structure = [
'(', '(', '+', '(', '(', '+', '(', '+', '(', '(', '+', '.', '(',
'(', '+', '.', '(', '(', '+', ')', ')', ')', ')', ')', '+', ')',
')', ')', ')', ')', ')', '.'
]
foo = objects.Complex(sequence=sequence, structure=structure)
fooIO = objects.TestTubeIO(
objects.TestTube(complexes={foo.name: (foo, float("inf"), None)}))
#fooIO.write_dnafile(sys.stdout)
f = open(os.devnull, "w")
fooIO.write_dnafile(f)
def test_rotations(self):
foo = objects.Complex(sequence=[
self.d1, self.d2, self.d3, '+', self.d1, '+', self.d1c, self.d3c,
self.d1c, self.d2
],
structure=list('..(+(+))..'))
self.assertEqual(foo.rotate_once, foo)
self.assertEqual(foo.sequence, [
self.d1, '+', self.d1c, self.d3c, self.d1c, self.d2, '+', self.d1,
self.d2, self.d3
])
self.assertEqual(foo.structure, list('(+)(..+..)'))
self.assertEqual(foo.nucleotide_sequence,
list('YYYYY+RRRRRYYYYYRRRRRNNNNN+YYYYYNNNNNRRRRR'))
for r in foo.rotate:
self.assertEqual(r, foo)
self.assertEqual(foo.sequence, [
self.d1, '+', self.d1c, self.d3c, self.d1c, self.d2, '+', self.d1,
self.d2, self.d3
])
self.assertEqual(foo.structure, list('(+)(..+..)'))
self.assertEqual(foo.nucleotide_sequence,
list('YYYYY+RRRRRYYYYYRRRRRNNNNN+YYYYYNNNNNRRRRR'))