def do_mutation(self, solution: MSASolution) -> MSASolution:
if random.random() <= self.probability:
# Select one random sequence from all
for seq in range(solution.number_of_variables):
gaps_group = solution.gaps_groups[seq]
if len(gaps_group) >= 4:
random_gaps_group = random.randrange(
0,
len(gaps_group) - 2, 2)
shift_to = -1 if random.randint(0, 1) == 0 else 1
gaps_group[random_gaps_group] += shift_to
gaps_group[random_gaps_group + 1] += shift_to
solution.merge_gaps_groups()
if self.remove_full_of_gap_columns:
solution.remove_full_of_gaps_columns()
# Sanity check: alignment is valid (same length for all sequences)
if not solution.is_valid_msa():
raise Exception("Mutated solution is not valid! {0}".format(
solution.decode_alignment_as_list_of_pairs()))
return solution
def do_mutation(self, solution: MSASolution) -> MSASolution:
if random.random() <= self.probability:
if solution.number_of_variables >= 1:
seq = random.randint(0, solution.number_of_variables - 1)
else:
seq = 0
gaps_group = solution.gaps_groups[seq]
if len(gaps_group) >= 4:
random_gaps_group = random.randrange(0, len(gaps_group) - 2, 2)
right_is_closest = False
if not right_is_closest:
to_add = gaps_group[random_gaps_group +
3] - gaps_group[random_gaps_group +
2] + 1
gaps_group[random_gaps_group + 1] += to_add
del gaps_group[random_gaps_group + 3]
del gaps_group[random_gaps_group + 2]
solution.merge_gaps_groups()
if self.remove_full_of_gap_columns:
solution.remove_full_of_gaps_columns()
# Sanity check: alignment is valid (same length for all sequences)
if not solution.is_valid_msa():
raise Exception("Mutated solution is not valid! {0}".format(
solution.decode_alignment_as_list_of_pairs()))
return solution
def test_should_merge_gaps_groups_case_b(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1']
problem.number_of_variables = 1
aln_seq = [('seq1', 'ACTGAC')]
msa = MSASolution(problem, msa=aln_seq)
msa.gaps_groups[0] = [2, 4, 4, 8, 8, 10]
self.assertEqual(["AC-----------TGAC"],
msa.decode_alignment_as_list_of_sequences())
# run
msa.merge_gaps_groups()
# check
self.assertEqual([2, 10], msa.gaps_groups[0])
def test_should_merge_gaps_groups(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2']
problem.number_of_variables = 2
aln_seq = [('seq1', 'ACTGAC'), ('seq2', 'ATCTC')]
msa = MSASolution(problem, msa=aln_seq)
msa.gaps_groups[0] = [2, 4, 4, 5]
msa.gaps_groups[1] = [2, 4, 5, 8]
self.assertEqual(["AC-----TGAC", "AT-------CTC"],
msa.decode_alignment_as_list_of_sequences())
# run
msa.merge_gaps_groups()
# check
self.assertEqual([2, 5], msa.gaps_groups[0])
self.assertEqual([2, 8], msa.gaps_groups[1])