def test_inherit_feature_delete(self):
orig = Component('TTACCCATT', features=[SeqFeature(FeatureLocation(0, 1), type='tt')])
f = orig.features.add(FeatureLocation(3, 6), type='ccc')
self.assertEqual('CCC', str(f.seq))
mutated = orig.mutate([DEL(3, 3)])
self.assertEqual('TTAATT', str(mutated.seq))
self.assertEqual([Feature(mutated, FeatureLocation(0, 1), type='tt')], list(mutated.features))
def test_feature_non_strict_order(self):
"""
In non-strict mode, potentially ambiguous mutations are allowed where the order in which
the order in which the mutations are applied is significant.
"""
component = Component('12345', feature_class=Feature)
component.features.add(FeatureLocation(2, 4), type='34')
# |████| |████|
# 12|3 4|5 12|3 4|5
# 12|3xy4|5 12|3 -|5
# 12|3xy|-5 12|3 xy|5
mutated_1 = component.mutate([DEL(3), INS(3, 'xy')], strict=False)
self.assertEqual('3xy', str(list(mutated_1.features)[0].seq)) # 3 would also be acceptable.
self.assertEqual('123xy5', str(mutated_1.seq))
mutated_2 = component.mutate([INS(3, 'xy'), DEL(3)], strict=False)
self.assertEqual('3xy', str(list(mutated_2.features)[0].seq))
self.assertEqual('123xy5', str(mutated_2.seq))
def test_lineage_simple(self):
generation1 = Component('Ax')
generation2 = generation1.mutate([INS(1, 'B')])
generation3 = generation2.mutate([INS(2, 'C')])
other = Component('a')
self.assertEqual('ABx', str(generation2.seq))
self.assertEqual(False, generation1.inherits_from(generation3))
self.assertEqual(True, generation3.inherits_from(generation1))
self.assertEqual(False, generation3.inherits_from(other))
self.assertEqual([generation2, generation1], list(generation3.get_lineage()))
def test_inherit_features(self):
component = Component('ABCDEFGHIerrorJKLMNOPQRSTUVXYZ')
component.features.add(FeatureLocation(0, 3), id='abc') # fine
component.features.add(FeatureLocation(9, 14), id='error') # fine
component.features.add(FeatureLocation(6, 12), id='GHI..err')
component.features.add(FeatureLocation(11, 17), id='ror..JKL')
component.features.add(FeatureLocation(8, 15), id='I..error..J') # fine
component.features.add(FeatureLocation(29, 30), id='end') # fine
mutated = component.mutate([DEL(9, 5)])
self.assertEqual({'JKL', 'Z', 'ABC', 'GHI', 'IJ'}, set(str(f.seq) for f in mutated.features))
def test_feature_non_strict_order(self):
"""
In non-strict mode, potentially ambiguous mutations are allowed where the order in which
the order in which the mutations are applied is significant.
"""
component = Component('12345', feature_class=Feature)
component.features.add(FeatureLocation(2, 4), type='34')
# |████| |████|
# 12|3 4|5 12|3 4|5
# 12|3xy4|5 12|3 -|5
# 12|3xy|-5 12|3 xy|5
mutated_1 = component.mutate([DEL(3), INS(3, 'xy')], strict=False)
self.assertEqual('3xy', str(list(
mutated_1.features)[0].seq)) # 3 would also be acceptable.
self.assertEqual('123xy5', str(mutated_1.seq))
mutated_2 = component.mutate([INS(3, 'xy'), DEL(3)], strict=False)
self.assertEqual('3xy', str(list(mutated_2.features)[0].seq))
self.assertEqual('123xy5', str(mutated_2.seq))
def test_lineage_simple(self):
generation1 = Component('Ax')
generation2 = generation1.mutate([INS(1, 'B')])
generation3 = generation2.mutate([INS(2, 'C')])
other = Component('a')
self.assertEqual('ABx', str(generation2.seq))
self.assertEqual(False, generation1.inherits_from(generation3))
self.assertEqual(True, generation3.inherits_from(generation1))
self.assertEqual(False, generation3.inherits_from(other))
self.assertEqual([generation2, generation1],
list(generation3.get_lineage()))
def test_inherited_search(self):
letters = Component('AABBDDEE', features=[
SeqFeature(FeatureLocation(0, 1), type='vowel'),
SeqFeature(FeatureLocation(2, 5), type='consonant'),
SeqFeature(FeatureLocation(5, 6), type='vowel')])
letters = letters.mutate([INS(4, 'CC')])
self.assertEqual('AABBCCDDEE', str(letters.seq))
self.assertEqual([Feature(letters, FeatureLocation(0, 1), type='vowel'),
Feature(letters, FeatureLocation(7, 8), type='vowel')],
list(letters.features.find(type='vowel')))
self.assertEqual([], list(letters.features.find(type='consonant', between_end=1)))
def test_mutate_1(self):
component = Component('ABCDEFGHIJKLMNOPQRSTUVWXYZ')
# . . . . . .
mutated = component.mutate( # 01234567 8901234567890 12345
[SNP(3, 'd'), # ABCdEFGH IJKLMNOPQRSTU VWXYZ
DEL(1), # A-CdEFGH IJKLMNOPQRSTU VWXYZ
INS(21, 'xx'), # A-CdEFGH IJKLMNOPQRSTUxxVWXYZ
Mutation(10, 9, 'oops'), # A-CdEFGH IJoops-----TUxxVWXYZ
SUB(4, 'ef'), # A-CdefGH IJoops-----TUxxVWXYZ
Mutation(7, 1, 'Hh')], # A-CdefGHhIJoops-----TUxxVWXYZ
strict=False) # 0 1234567890123 457890123
# . . . . .
self.assertEqual('ACdefGHhIJoopsTUxxVWXYZ', str(mutated.seq))
def test_inherit_features(self):
component = Component('ABCDEFGHIerrorJKLMNOPQRSTUVXYZ')
component.features.add(FeatureLocation(0, 3), id='abc') # fine
component.features.add(FeatureLocation(9, 14), id='error') # fine
component.features.add(FeatureLocation(6, 12), id='GHI..err')
component.features.add(FeatureLocation(11, 17), id='ror..JKL')
component.features.add(FeatureLocation(8, 15),
id='I..error..J') # fine
component.features.add(FeatureLocation(29, 30), id='end') # fine
mutated = component.mutate([DEL(9, 5)])
self.assertEqual({'JKL', 'Z', 'ABC', 'GHI', 'IJ'},
set(str(f.seq) for f in mutated.features))
def test_inherit_feature_delete(self):
orig = Component(
'TTACCCATT',
features=[SeqFeature(FeatureLocation(0, 1), type='tt')])
f = orig.features.add(FeatureLocation(3, 6), type='ccc')
self.assertEqual('CCC', str(f.seq))
mutated = orig.mutate([DEL(3, 3)])
self.assertEqual('TTAATT', str(mutated.seq))
self.assertEqual([Feature(mutated, FeatureLocation(0, 1), type='tt')],
list(mutated.features))
def test_quickstart_feature_inherit(self):
slogan = Component('CoPy is for DNA components', features=[
SeqFeature(FeatureLocation(0, 4), type='name'),
SeqFeature(FeatureLocation(12, 15), id='DNA')])
self.assertEqual('components', str(slogan.features.add(FeatureLocation(16, 26)).seq))
self.assertEqual(['CoPy', 'DNA', 'components'], [str(f.seq) for f in slogan.features])
new_slogan = slogan.mutate([DEL(2, 2), DEL(12, 4)])
self.assertEqual('Co is for components', str(new_slogan.seq))
self.assertEqual([Feature(new_slogan, FeatureLocation(0, 2), type='name'),
Feature(new_slogan, FeatureLocation(10, 20))], list(new_slogan.features))
self.assertEqual(['Co', 'components'], [str(f.seq) for f in new_slogan.features])
def test_mutate_1(self):
component = Component('ABCDEFGHIJKLMNOPQRSTUVWXYZ')
# . . . . . .
mutated = component.mutate( # 01234567 8901234567890 12345
[
SNP(3, 'd'), # ABCdEFGH IJKLMNOPQRSTU VWXYZ
DEL(1), # A-CdEFGH IJKLMNOPQRSTU VWXYZ
INS(21, 'xx'), # A-CdEFGH IJKLMNOPQRSTUxxVWXYZ
Mutation(10, 9, 'oops'), # A-CdEFGH IJoops-----TUxxVWXYZ
SUB(4, 'ef'), # A-CdefGH IJoops-----TUxxVWXYZ
Mutation(7, 1, 'Hh')
], # A-CdefGHhIJoops-----TUxxVWXYZ
strict=False) # 0 1234567890123 457890123
# . . . . .
self.assertEqual('ACdefGHhIJoopsTUxxVWXYZ', str(mutated.seq))
def test_quickstart_feature_inherit(self):
slogan = Component('CoPy is for DNA components',
features=[
SeqFeature(FeatureLocation(0, 4), type='name'),
SeqFeature(FeatureLocation(12, 15), id='DNA')
])
self.assertEqual('components',
str(slogan.features.add(FeatureLocation(16, 26)).seq))
self.assertEqual(['CoPy', 'DNA', 'components'],
[str(f.seq) for f in slogan.features])
new_slogan = slogan.mutate([DEL(2, 2), DEL(12, 4)])
self.assertEqual('Co is for components', str(new_slogan.seq))
self.assertEqual([
Feature(new_slogan, FeatureLocation(0, 2), type='name'),
Feature(new_slogan, FeatureLocation(10, 20))
], list(new_slogan.features))
self.assertEqual(['Co', 'components'],
[str(f.seq) for f in new_slogan.features])
def test_inherited_search(self):
letters = Component('AABBDDEE',
features=[
SeqFeature(FeatureLocation(0, 1),
type='vowel'),
SeqFeature(FeatureLocation(2, 5),
type='consonant'),
SeqFeature(FeatureLocation(5, 6), type='vowel')
])
letters = letters.mutate([INS(4, 'CC')])
self.assertEqual('AABBCCDDEE', str(letters.seq))
self.assertEqual([
Feature(letters, FeatureLocation(0, 1), type='vowel'),
Feature(letters, FeatureLocation(7, 8), type='vowel')
], list(letters.features.find(type='vowel')))
self.assertEqual([],
list(
letters.features.find(type='consonant',
between_end=1)))