def test_mutate_insert(self):
self.assertEqual('99012345',
str(Component('012345').mutate([INS(0, '99')]).seq))
self.assertEqual('09912345',
str(Component('012345').mutate([INS(1, '99')]).seq))
self.assertEqual(
'9912345',
str(Component('012345').mutate([INS(0, '99', replace=True)]).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_from_mutations_simple(self):
tt = MutableTranslationTable.from_mutations(
'ABCDEFGHI', (DEL(1, 2), INS(7, 'insert')))
self.assertEqual([0, None, None, 1, 2, 9, 10, 11, 12], list(tt))
self.assertEqual(
[0, 3, 4, None, None, None, None, None, None, 5, 6, 7, 8],
list(~tt))
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_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_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)))
from co.converters import GenbankConverter
from co.mutation import DEL, INS
component = GenbankConverter.from_file('NC_000913_3.gb')
updated_component = component.mutate([
DEL(2173363 - 1, 2),
INS(3560456 - 1, 'G'),
INS(4296381 - 1, 'CG')
])
GenbankConverter.to_file(updated_component, 'bop27.gb')