>>> s = DNA('GG-GG')
>>> for motif_slice in s.find_motifs('purine-run', ignore=s.gaps()):
... motif_slice
slice(0, 5, None)
"""
if motif_type not in self._motifs:
raise ValueError("Not a known motif (%r) for this sequence (%s)." %
(motif_type, self.__class__.__name__))
return self._motifs[motif_type](self, min_length, ignore)
@overrides(Sequence)
def _constructor(self, **kwargs):
return self.__class__(validate=False, lowercase=False, **kwargs)
@overrides(Sequence)
def _repr_stats(self):
"""Define custom statistics to display in the sequence's repr."""
stats = super(IUPACSequence, self)._repr_stats()
stats.append(('has gaps', '%r' % self.has_gaps()))
stats.append(('has degenerates', '%r' % self.has_degenerates()))
stats.append(('has non-degenerates', '%r' % self.has_nondegenerates()))
return stats
_motifs = MiniRegistry()
# Leave this at the bottom
_motifs.interpolate(IUPACSequence, "find_motifs")
class TestMiniRegistry(unittest.TestCase):
def setUp(self):
self.registry = MiniRegistry()
def test_decoration(self):
self.assertNotIn("name1", self.registry)
self.assertNotIn("name2", self.registry)
self.n1_called = False
self.n2_called = False
@self.registry("name1")
def some_registration1():
self.n1_called = True
@self.registry("name2")
def some_registration2():
self.n2_called = True
self.assertIn("name1", self.registry)
self.assertEqual(some_registration1, self.registry["name1"])
self.assertIn("name2", self.registry)
self.assertEqual(some_registration2, self.registry["name2"])
self.registry["name1"]()
self.assertTrue(self.n1_called)
self.registry["name2"]()
self.assertTrue(self.n2_called)
def test_copy(self):
@self.registry("name")
def some_registration():
pass
new = self.registry.copy()
self.assertIsNot(new, self.registry)
@new("other")
def other_registration():
pass
self.assertIn("name", self.registry)
self.assertNotIn("other", self.registry)
self.assertIn("other", new)
self.assertIn("name", new)
def test_everything(self):
class SomethingToInterpolate(object):
def interpolate_me():
"""First line
Some description of things, also this:
Other things are happening now.
"""
def dont_interpolate_me():
"""First line
Some description of things, also this:
Other things are happening now.
"""
class Subclass(SomethingToInterpolate):
pass
@self.registry("a")
def a():
"""x"""
@self.registry("b")
def b():
"""y"""
@self.registry("c")
def c():
"""z"""
subclass_registry = self.registry.copy()
@subclass_registry("o")
def o():
"""p"""
self.registry.interpolate(SomethingToInterpolate, "interpolate_me")
subclass_registry.interpolate(Subclass, "interpolate_me")
self.assertEqual(SomethingToInterpolate.interpolate_me.__doc__,
"First line\n\n Some description of th"
"ings, also this:\n\n\t'a'\n\t x\n\t'b'\n\t y\n\t'c"
"'\n\t z\n\n Other things are happeni"
"ng now.\n ")
self.assertEqual(SomethingToInterpolate.dont_interpolate_me.__doc__,
"First line\n\n Some description of th"
"ings, also this:\n\n Other things are"
" happening now.\n ")
self.assertEqual(Subclass.interpolate_me.__doc__,
"First line\n\n Some description of th"
"ings, also this:\n\n\t'a'\n\t x\n\t'b'\n\t y\n\t'c"
"'\n\t z\n\t'o'\n\t p\n\n Other thin"
"gs are happening now.\n ")
self.assertEqual(Subclass.dont_interpolate_me.__doc__,
"First line\n\n Some description of th"
"ings, also this:\n\n Other things are"
" happening now.\n ")
def setUp(self):
self.registry = MiniRegistry()
def setUp(self):
self.registry = MiniRegistry()
class TestMiniRegistry(unittest.TestCase):
def setUp(self):
self.registry = MiniRegistry()
def test_decoration(self):
self.assertNotIn("name1", self.registry)
self.assertNotIn("name2", self.registry)
self.n1_called = False
self.n2_called = False
@self.registry("name1")
def some_registration1():
self.n1_called = True
@self.registry("name2")
def some_registration2():
self.n2_called = True
self.assertIn("name1", self.registry)
self.assertEqual(some_registration1, self.registry["name1"])
self.assertIn("name2", self.registry)
self.assertEqual(some_registration2, self.registry["name2"])
self.registry["name1"]()
self.assertTrue(self.n1_called)
self.registry["name2"]()
self.assertTrue(self.n2_called)
def test_copy(self):
@self.registry("name")
def some_registration():
pass
new = self.registry.copy()
self.assertIsNot(new, self.registry)
@new("other")
def other_registration():
pass
self.assertIn("name", self.registry)
self.assertNotIn("other", self.registry)
self.assertIn("other", new)
self.assertIn("name", new)
def test_everything(self):
class SomethingToInterpolate(object):
def interpolate_me():
"""First line
Some description of things, also this:
Other things are happening now.
"""
def dont_interpolate_me():
"""First line
Some description of things, also this:
Other things are happening now.
"""
class Subclass(SomethingToInterpolate):
pass
@self.registry("a")
def a():
"""x"""
@self.registry("b")
def b():
"""y"""
@self.registry("c")
def c():
"""z"""
subclass_registry = self.registry.copy()
@subclass_registry("o")
def o():
"""p"""
self.registry.interpolate(SomethingToInterpolate, "interpolate_me")
subclass_registry.interpolate(Subclass, "interpolate_me")
self.assertEqual(
SomethingToInterpolate.interpolate_me.__doc__,
"First line\n\n Some description of th"
"ings, also this:\n\n\t'a'\n\t x\n\t'b'\n\t y\n\t'c"
"'\n\t z\n\n Other things are happeni"
"ng now.\n ")
self.assertEqual(
SomethingToInterpolate.dont_interpolate_me.__doc__,
"First line\n\n Some description of th"
"ings, also this:\n\n Other things are"
" happening now.\n ")
self.assertEqual(
Subclass.interpolate_me.__doc__,
"First line\n\n Some description of th"
"ings, also this:\n\n\t'a'\n\t x\n\t'b'\n\t y\n\t'c"
"'\n\t z\n\t'o'\n\t p\n\n Other thin"
"gs are happening now.\n ")
self.assertEqual(
Subclass.dont_interpolate_me.__doc__,
"First line\n\n Some description of th"
"ings, also this:\n\n Other things are"
" happening now.\n ")
>>> s = DNA('GG-GG')
>>> for motif_slice in s.find_motifs('purine-run', ignore=s.gaps()):
... motif_slice
slice(0, 5, None)
"""
if motif_type not in self._motifs:
raise ValueError("Not a known motif (%r) for this sequence (%s)." %
(motif_type, self.__class__.__name__))
return self._motifs[motif_type](self, min_length, ignore)
@overrides(Sequence)
def _constructor(self, **kwargs):
return self.__class__(validate=False, lowercase=False, **kwargs)
@overrides(Sequence)
def _repr_stats(self):
"""Define custom statistics to display in the sequence's repr."""
stats = super(GrammaredSequence, self)._repr_stats()
stats.append(('has gaps', '%r' % self.has_gaps()))
stats.append(('has degenerates', '%r' % self.has_degenerates()))
stats.append(('has definites', '%r' % self.has_definites()))
return stats
_motifs = MiniRegistry()
# Leave this at the bottom
_motifs.interpolate(GrammaredSequence, "find_motifs")
>>> s = DNA('GG-GG')
>>> for motif_slice in s.find_motifs('purine-run', ignore=s.gaps()):
... motif_slice
slice(0, 5, None)
"""
if motif_type not in self._motifs:
raise ValueError("Not a known motif (%r) for this sequence (%s)." %
(motif_type, self.__class__.__name__))
return self._motifs[motif_type](self, min_length, ignore)
@overrides(Sequence)
def _constructor(self, **kwargs):
return self.__class__(validate=False, lowercase=False, **kwargs)
@overrides(Sequence)
def _repr_stats(self):
"""Define custom statistics to display in the sequence's repr."""
stats = super(GrammaredSequence, self)._repr_stats()
stats.append(('has gaps', '%r' % self.has_gaps()))
stats.append(('has degenerates', '%r' % self.has_degenerates()))
stats.append(('has definites', '%r' % self.has_definites()))
return stats
_motifs = MiniRegistry()
# Leave this at the bottom
_motifs.interpolate(GrammaredSequence, "find_motifs")
>>> s = DNA('GG-GG')
>>> for motif_slice in s.find_motifs('purine-run', ignore=s.gaps()):
... motif_slice
slice(0, 5, None)
"""
if motif_type not in self._motifs:
raise ValueError("Not a known motif (%r) for this sequence (%s)." %
(motif_type, self.__class__.__name__))
return self._motifs[motif_type](self, min_length, ignore)
@overrides(Sequence)
def _constructor(self, **kwargs):
return self.__class__(validate=False, lowercase=False, **kwargs)
@overrides(Sequence)
def _repr_stats(self):
"""Define custom statistics to display in the sequence's repr."""
stats = super(IUPACSequence, self)._repr_stats()
stats.append(('has gaps', '%r' % self.has_gaps()))
stats.append(('has degenerates', '%r' % self.has_degenerates()))
stats.append(('has non-degenerates', '%r' % self.has_nondegenerates()))
return stats
_motifs = MiniRegistry()
# Leave this at the bottom
_motifs.interpolate(IUPACSequence, "find_motifs")
