def test_should_single_point_crossover_work_properly_case_g(self, random_call):
""" Example of MSA in Ortuño's paper
GKGD---PK|KP, GKGD-PK|KP => GKGD---PK-KP, GKGD-PK--KP
M------QD|RV, --M--QD|RV => M------QD-RV, --M--QD--RV
MKKLKKHPD|FP, MKKLKKHPD|FP => MKKLKKHPD-FP, MKKLKKHPDFP
M--------|HI, ---M--H|I- => M--------HI-, ---M--H---I """
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3', 'seq4']
problem.number_of_variables = 4
msa_1 = MSASolution(problem, msa=[('seq1', 'GKGD---PKKP'), ('seq2', 'M------QDRV'),
('seq3', 'MKKLKKHPDFP'), ('seq4', 'M--------HI')])
msa_2 = MSASolution(problem, msa=[('seq1', 'GKGD-PKKP'), ('seq2', '--M--QDRV'),
('seq3', 'MKKLKKHPDFP'), ('seq4', '---M--HI-')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
random_call.return_value = 8
children = crossover.execute([msa_1, msa_2])
# check
self.assertEqual(["GKGD---PK-KP", "M------QD-RV", "MKKLKKHPD-FP", "M--------HI-"],
children[0].decode_alignment_as_list_of_sequences())
self.assertEqual(["GKGD-PK--KP", "--M--QD--RV", "MKKLKKHPDFP", "---M--H---I"],
children[1].decode_alignment_as_list_of_sequences())
def test_should_single_point_crossover_work_properly_real_case(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['a', 'b', 'c', 'd']
problem.number_of_variables = 4
msa_1 = MSASolution(problem, msa=[
('a', '----GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPK----------GE'),
('b', '-------MQDRVKRPMNAFIVWSRDQRRKMALENPRMRN--SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK'),
('c', 'MKKLK---KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDH---PDLIQNAKK'),
('d', '---------MHIKKPLNAFMLYMKEMRANVVAESTLKES--AAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK')
])
msa_2 = MSASolution(problem, msa=[
('a', '----GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPK---GE-------'),
('b', '----M---QDRVKRPMNAFIVWSRDQRRKMALENPRMRN--SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP---RRKAKMLPK'),
('c', 'MKKLK-KHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSN--LDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDH---PDLIQNAKK'),
('d', '-------MH--IKKPLNAFMLYMKEMRANVVAESTLKES--AAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK')
])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
children = crossover.cross_parents(10, [msa_1, msa_2], [10, 10, 10, 10], [10, 10, 8, 8])
# check
self.assertTrue(children[0].is_valid_msa())
self.assertTrue(children[1].is_valid_msa())
def find_length_of_the_largest_sequence(self, solution: MSASolution):
max_length = solution.get_length_of_sequence(0)
for i in range(1, solution.number_of_variables):
length_of_sequence_i = solution.get_length_of_sequence(i)
if max_length < length_of_sequence_i:
max_length = length_of_sequence_i
return max_length
def test_should_return_number_of_gaps_of_one_sequences(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa = MSASolution(problem,
msa=[('seq1', 'AC---TGAC'), ('seq2', 'AT--CT--C'),
('seq3', 'AAC---TGC')])
# check
self.assertEqual(3, msa.get_number_of_gaps_of_sequence_at_index(0))
def test_should_return_original_alignment_size(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa = MSASolution(problem,
msa=[('seq1', 'AC---TGAC'), ('seq2', 'AT--CT--C'),
('seq3', 'AAC---TGC')])
# check
self.assertEqual(9, msa.get_length_of_alignment())
def evaluate(self, solution: MSASolution) -> MSASolution:
solution.remove_full_of_gaps_columns()
sequences = solution.decode_alignment_as_list_of_sequences()
for i, score in enumerate(self.score_list):
solution.objectives[i] = score.compute(sequences)
if not score.is_minimization():
solution.objectives[i] = -solution.objectives[i]
return solution
def test_should_return_gap_columns(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa = MSASolution(problem,
msa=[('seq1', '--AA-'), ('seq2', '--AA-'),
('seq3', '--AA-')])
# check
self.assertEqual([0, 1, 4], msa.get_gap_columns_from_alignment())
def test_should_return_original_sequences(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa = MSASolution(problem,
msa=[('seq1', 'AC---TGAC'), ('seq2', 'AT--CT--C'),
('seq3', 'AAC---TGC')])
# check
self.assertEqual(['AC---TGAC', 'AT--CT--C', 'AAC---TGC'],
msa.decode_alignment_as_list_of_sequences())
def test_should_return_is_gap_column(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa = MSASolution(problem,
msa=[('seq1', 'AC---TGAC'), ('seq2', 'AT--CT--C'),
('seq3', 'AAC---TGC')])
# check
self.assertTrue(msa.is_gap_column(3))
self.assertFalse(msa.is_gap_column(4))
def test_should_single_point_crossover_work_properly_real_case(self, random_call):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['1bbt_ac', '1al2_ad', '1b35_C', '1bbt_ab', '1mec_aa', '1bbt_aa', '1al2_ab',
'1al2_ac']
problem.number_of_variables = 8
msa_1 = MSASolution(problem, msa=[
('1bbt_ac',
'------GIFPVACSDGYGGLVTTDPKTAD---PVYGKVFNPPRNQLPGRFTNLLDVAEACP--------TFLRFEGGVPYVTTKTDSDRVLAQFDMSL----AAKHMSNTFLAG---------------------LAQYYTQYSGT-----INLHFMFTGPTDAKA-------RYMVAY----APPGMEPPKTPEAAAH---------------CIHAEWDTGLNSKF---------TFSIPYLSAADYT----YTASDVAETTNV--------QGWVCLFQ--------ITHGKADG-------DALVVLASAGKDF-----------------------ELRLPVDARAE----'),
('1al2_ad',
'-------GLPVMNTPGSNQYLTADNFQSP---CALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDL--SATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGE---------------------ILNYYTHWAGS-----LKFTFLFCGSMMATG-------KLLVSY----APPGADPPKKRKEAML---------------GTHVIWDIGLQSSC---------TMVVPWISNTT------YRQTIDDSFTE---------GGYISVFYQTRIV---VPLSTPRE-------MDILGFVSACNDF-----------------------SVRLLRDTTHIEQKA'),
('1b35_C',
'SKPTVQGKIGECKLRGQGRMANFDGMDMSHKMALSSTNEIETNEGLAGTSLDVMDLSRVLSIPNYWDRFTWKTSDVINTVLWDNYVSPFKVKPYSATI-----TDRFRCTHMGK---------------------VANAFTYWRGS-----MVYTFKFVKTQYHSG---RLRISFIPYYYNTTISTGTPDVSRTQKI---------------------VVDLRTSTAV---------SFTVPYIGSRPWLYCIRPESSWLSKDNTDGALMYNCVSGIVRVEVLNQLVAAQNVFSEIDVICEVNGGPDLEFAGPTCPRY----------VPYAGDFTLADTRKIEAERTQEYSNNED'),
('1bbt_ab',
'-------LLEDRILTTRNGHTTSTTQSS----VGVTYGYATAEDFVSGPNTSGLETRVV----------QAERFFKTHLFDWVTSDSFGRCHLLELPT---------DHKGVYGS--------------------LTDSYAYMRNG-----WDVEVTAVGNQFNGG-------CLLVAM----VPELCSIQKRELYQLT--------------LFPHQFINPRTNMTA---------HITVPFVGVNR------YDQYKVHKP-----------WTLVVMVVAPLTV---NTEGAPQI-------KVYANIAPTNVHV-----------------------AGEFPSKE-------'),
('1mec_aa',
'------------------GVENAEKGVTEN--TDATADFVAQPVYLPENQTKVAFFYDRSSPIGRFAVKSGSLESGFAPFSNKACPNSVILTPGPQFDPAYDQLRPQRLTEIWGNGNEETSEVFPLKTKQDYSFCLFSPFVYYKCD-----LEVTLSPHTSGAHGL---------LVRW----CPTGTPTKPTTQVLHEVSSLSEGRT------PQVYSAGPGTSNQI---------SFVVPYNSPLSVLPAVWYNGHKRFDNTGD--------LGIAPNSDFGTLF---FAGTKPDI-------KFTVYLRYKNMRVFCPRP--TVFFPWPT----SGDKIDMTPRAGVL-----'),
('1bbt_aa',
'---------------------TTSAGESADPVTTTVENYGGETQIQRRQHTDVSFI--------------------MDRFVKVTPQNQINILDLMQVP---------SHTLVGG---------------------LLRASTYYFSD-----LEIAVK------HEG---------DLTW----VPNGAPEK---------------------------ALDNTTNPTAYHKAPLT--RLALPYTAPHRVLATV-YNGECRTLPTSFN-------YGAIKATRVTELL---YRMKRAETYCP----RPLLAIHPTEARH---------------------KQKIVAP----------'),
('1al2_ab',
'------AATSRDALPNTEASGPTHSKEIP---ALTAVETGATNPLVPSDTVQTRHVVQH----------RSRSESSIESFFARGACVTIMTVDNPAST-----TNKDKLFAVWKITYKDTVQLRR----------KLEFFTYSRFD-----MELTFVVTANFTETNNGHALNQVYQIMY----IPPGAPVP----EKWD-----------------DYTWQTSSNPSIFYTYGTAPARISVPYVGISN-AYSHFYDGFSKVPLKDQSAALGDSLYGAASLNDFGILAVRVVNDHNPTKVT----SKIRVYLKPKHIRVWCPRPPRAVAYYGPGVDYKDGTLTPLSTKDLTTY----'),
('1al2_ac',
'----EACGYSDRVLQLTLGNSTITTQEA----ANSVVAYGRWPEYLRDSEANPVDQPTEPDV-------AACRFYTLDTVSWTKESRGWWWKLPDALRDMGLFGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNANPGEKGG-------TFTGTF----TPDNNQTSPARRFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCA---------TLVLPYVNSLS------IDSMVKHNN-----------WGIAILPLAPLNF---ASESSPEI-------PITLTIAPMCCEF-------------------NGLRNITLPRLQ-------'),
])
msa_2 = MSASolution(problem, msa=[
('1bbt_ac',
'------GIFPVACSDGYGGLVTTDPKTAD---PVYGKVFNPPRNQLPGRFTNLLDVAEACP--------TFLRFEGGVPYVTTKTDSDRVLAQFDMSL----AAKHMSNTFLAG---------------------LAQYYTQYSGT-----INLHFMFTGPTDAKA-------RYMVAY----APPGMEPPKTPEAAAH---------------CIHAEWDTGLNSKF---------TFSIPYLSAADYT----YTASDVAETTNV--------QGWVCLFQ--------ITHGKADG-------DALVVLASAGKDF-----------------------ELRLPVDARAE----'),
('1al2_ad',
'-------GLPVMNTPGSNQYLTADNFQSP---CALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDL--SATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTMLGE---------------------ILNYYTHWAGS-----LKFTFLFCGSMMATG-------KLLVSY----APPGADPPKKRKEAML---------------GTHVIWDIGLQSSC---------TMVVPWISNTT------YRQTIDDSFTE---------GGYISVFYQTRIV---VPLSTPRE-------MDILGFVSACNDF-----------------------SVRLLRDTTHIEQKA'),
('1b35_C',
'SKPTVQGKIGECKLRGQGRMANFDGMDMSHKMALSSTNEIETNEGLAGTSLDVMDLSRVLSIPNYWDRFTWKTSDVINTVLWDNYVSPFKVKPYSATI-----TDRFRCTHMGK---------------------VANAFTYWRGS-----MVYTFKFVKTQYHSG---RLRISFIPYYYNTTISTGTPDVSRTQKI---------------------VVDLRTSTAV---------SFTVPYIGSRPWLYCIRPESSWLSKDNTDGALMYNCVSGIVRVEVLNQLVAAQNVFSEIDVICEVNGGPDLEFAGPTCPRY----------VPYAGDFTLADTRKIEAERTQEYSNNED'),
('1bbt_ab',
'-------LLEDRILTTRNGHTTSTTQSS----VGVTYGYATAEDFVSGPNTSGLETRVV----------QAERFFKTHLFDWVTSDSFGRCHLLELPT---------DHKGVYGS--------------------LTDSYAYMRNG-----WDVEVTAVGNQFNGG-------CLLVAM----VPELCSIQKRELYQLT--------------LFPHQFINPRTNMTA---------HITVPFVGVNR------YDQYKVHKP-----------WTLVVMVVAPLTV---NTEGAPQI-------KVYANIAPTNVHV-----------------------AGEFPSKE-------'),
('1mec_aa',
'------------------GVENAEKGVTEN--TDATADFVAQPVYLPENQTKVAFFYDRSSPIGRFAVKSGSLESGFAPFSNKACPNSVILTPGPQFDPAYDQLRPQRLTEIWGNGNEETSEVFPLKTKQDYSFCLFSPFVYYKCD-----LEVTLSPHTSGAHGL---------LVRW----CPTGTPTKPTTQVLHEVSSLSEGRT------PQVYSAGPGTSNQI---------SFVVPYNSPLSVLPAVWYNGHKRFDNTGD--------LGIAPNSDFGTLF---FAGTKPDI-------KFTVYLRYKNMRVFCPRP--TVFFPWPT----SGDKIDMTPRAGVL-----'),
('1bbt_aa',
'---------------------TTSAGESADPVTTTVENYGGETQIQRRQHTDVSFI--------------------MDRFVKVTPQNQINILDLMQVP---------SHTLVGG---------------------LLRASTYYFSD-----LEIAVK------HEG---------DLTW----VPNGAPEK---------------------------ALDNTTNPTAYHKAPLT--RLALPYTAPHRVLATV-YNGECRTLPTSFN-------YGAIKATRVTELL---YRMKRAETYCP----RPLLAIHPTEARH---------------------KQKIVAP----------'),
('1al2_ab',
'------AATSRDALPNTEASGPTHSKEIP---ALTAVETGATNPLVPSDTVQTRHVVQH----------RSRSESSIESFFARGACVTIMTVDNPAST-----TNKDKLFAVWKITYKDTVQLRR----------KLEFFTYSRFD-----MELTFVVTANFTETNNGHALNQVYQIMY----IPPGAPVP----EKWD-----------------DYTWQTSSNPSIFYTYGTAPARISVPYVGISN-AYSHFYDGFSKVPLKDQSAALGDSLYGAASLNDFGILAVRVVNDHNPTKVT----SKIRVYLKPKHIRVWCPRPPRAVAYYGPGVDYKDGTLTPLSTKDLTTY----'),
('1al2_ac',
'----EACGYSDRVLQLTLGNSTITTQEA----ANSVVAYGRWPEYLRDSEANPVDQPTEPDV-------AACRFYTLDTVSWTKESRGWWWKLPDALRDMGLFGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNANPGEKGG-------TFTGTF----TPDNNQTSPARRFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCA---------TLVLPYVNSLS------IDSMVKHNN-----------WGIAILPLAPLNF---ASESSPEI-------PITLTIAPMCCEF-------------------NGLRNITLPRLQ-------'),
])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
random_call.return_value = 176
children = crossover.execute([msa_1, msa_2])
# check
self.assertTrue(children[0].is_valid_msa())
self.assertTrue(children[1].is_valid_msa())
def fill_sequences_with_gaps_to_reach_the_max_sequence_length(
self, solution: MSASolution, max_length: int,
cutting_points: list):
for i in range(solution.number_of_variables):
sequence_length = solution.get_length_of_sequence(i)
if sequence_length != max_length:
for j in range(sequence_length, max_length):
if cutting_points[i] == -1:
solution.add_gap_to_sequence_at_index(
seq_index=i, gap_position=sequence_length - 1)
else:
solution.add_gap_to_sequence_at_index(
seq_index=i, gap_position=cutting_points[i] + 1)
def test_should_remove_gap_column(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa = MSASolution(problem,
msa=[('seq1', 'AC---TGAC'), ('seq2', 'AT--CT--C'),
('seq3', 'AAC---TGC')])
msa.remove_gap_column(3)
# check
self.assertEqual([[2, 2, 4, 4], [2, 2, 6, 7], [4, 5]], msa.gaps_groups)
def test_should_remove_all_gap_columns_case_d(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2']
problem.number_of_variables = 2
msa = MSASolution(problem,
msa=[('seq1', 'AB--CDE-'), ('seq2', 'AB--CD-E')])
msa.remove_full_of_gaps_columns()
# check
self.assertEqual(['ABCDE-', 'ABCD-E'],
msa.decode_alignment_as_list_of_sequences())
def test_should_remove_all_gap_columns_case_b(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa = MSASolution(problem,
msa=[('seq1', 'AC--T--GC'), ('seq2', 'AC-----AC'),
('seq3', 'A---C--AC')])
msa.remove_full_of_gaps_columns()
# check
self.assertEqual(['ACTGC', 'AC-AC', 'A-CAC'],
msa.decode_alignment_as_list_of_sequences())
def find_cutting_points_in_first_parent(self, solution: MSASolution,
position: int) -> list:
""" Find the real cutting points in a solution. If the column is a gap then the next non-gap
symbol must be found """
positions = [-1 for _ in range(solution.number_of_variables)]
for i in range(solution.number_of_variables):
if solution.is_gap_char_at_sequence(i, position):
positions[i] = solution.get_next_char_position_after_gap(
i, position)
else:
positions[i] = position
return positions
def test_should_return_length_of_gaps_groups(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa_1 = MSASolution(problem,
msa=[('seq1', 'AC---TGAC'), ('seq2', 'AT--CT--C'),
('seq3', 'AAC---TGC')])
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3', 'seq4']
problem.number_of_variables = 4
msa_2 = MSASolution(problem,
msa=[('seq1', 'GKGD---PKKP'),
('seq2', 'M------QDRV'),
('seq3', 'MKKLKKHPDFP'),
('seq4', 'M--------HI-')])
# check
self.assertEqual(3, msa_1.get_length_of_gaps(0))
self.assertEqual(4, msa_1.get_length_of_gaps(1))
self.assertEqual(3, msa_1.get_length_of_gaps(2))
self.assertEqual(3, msa_2.get_length_of_gaps(0))
self.assertEqual(6, msa_2.get_length_of_gaps(1))
self.assertEqual(0, msa_2.get_length_of_gaps(2))
self.assertEqual(9, msa_2.get_length_of_gaps(3))
def do_mutation(self, solution: MSASolution) -> MSASolution:
if random.random() <= self.probability:
for i in range(solution.number_of_variables):
gaps_group = solution.gaps_groups[i]
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:
diff = (gaps_group[random_gaps_group + 3] - gaps_group[random_gaps_group + 2]) - \
(gaps_group[random_gaps_group + 1] - gaps_group[random_gaps_group])
if diff < 0:
# diff < 0 means that gaps group 2 is shorter than gaps group 1, thus we need to decrease
# the length of the gaps group 1
diff = -1 * diff
gaps_group[random_gaps_group + 1] -= diff
gaps_group[random_gaps_group + 3] += diff
# displace gaps group 2 one position to the left
gaps_group[random_gaps_group + 2] -= diff
gaps_group[random_gaps_group + 3] -= diff
elif diff > 0:
# diff > 0 means that gaps group 2 is larger than gaps group 1, thus we need to increase
# the length of the gaps group 1
gaps_group[random_gaps_group + 1] += diff
gaps_group[random_gaps_group + 3] -= diff
# displace gaps group 2 one position to the right
gaps_group[random_gaps_group + 2] += diff
gaps_group[random_gaps_group + 3] += diff
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_single_point_crossover_work_properly_case_j(self, random_call):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2']
problem.number_of_variables = 2
msa_1 = MSASolution(problem, msa=[('seq1', 'MIKMIM-IK'), ('seq2', 'A-B-CDEF-')])
msa_2 = MSASolution(problem, msa=[('seq1', '--MIKMIMIK'), ('seq2', 'ABC-D-E-F-')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=True)
# run
random_call.return_value = 2
children = crossover.execute([msa_1, msa_2])
# check
self.assertEqual(["MIK--MIMIK", "A-BCD-E-F-"], children[0].decode_alignment_as_list_of_sequences())
self.assertEqual(["--MIKMIM-IK", "AB----CDEF-"], children[1].decode_alignment_as_list_of_sequences())
def test_should_the_solution_remain_unchanged_if_the_probability_is_zero(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa_1 = MSASolution(problem, msa=[('seq1', 'ACTC'), ('seq2', 'A-TC'), ('seq3', 'A--C')])
msa_2 = MSASolution(problem, msa=[('seq1', 'CT-G'), ('seq2', '-T-G'), ('seq3', '-ATG')])
crossover = SPXMSA(probability=0.0, remove_gap_columns=False)
# run
offspring = crossover.execute([msa_1, msa_2])
# check
self.assertEqual([('seq1', 'ACTC'), ('seq2', 'A-TC'), ('seq3', 'A--C')],
offspring[0].decode_alignment_as_list_of_pairs())
self.assertEqual([('seq1', 'CT-G'), ('seq2', '-T-G'), ('seq3', '-ATG')],
offspring[1].decode_alignment_as_list_of_pairs())
def test_should_single_point_crossover_work_properly_case_c(self, random_call):
""" A|B-CD-EF, ---A|BCD-EF => ABCD-EF, ---AB-CD-EF """
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1']
problem.number_of_variables = 1
msa_1 = MSASolution(problem, msa=[('seq1', 'AB-CD-EF')])
msa_2 = MSASolution(problem, msa=[('seq1', '---ABCD-EF')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
random_call.return_value = 0
children = crossover.execute([msa_1, msa_2])
# check
self.assertEqual(["ABCD-EF"], children[0].decode_alignment_as_list_of_sequences())
self.assertEqual(["---AB-CD-EF"], children[1].decode_alignment_as_list_of_sequences())
def test_should_single_point_crossover_work_properly_case_h(self, random_call):
""" MSA with no crossover in the first sequence
-----------|-M, --M|------ => ------------M------, --M """
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1']
problem.number_of_variables = 1
msa_1 = MSASolution(problem, msa=[('seq1', '------------M')])
msa_2 = MSASolution(problem, msa=[('seq1', '--M------')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
random_call.return_value = 10
children = crossover.execute([msa_1, msa_2])
# check
self.assertEqual(["------------M------"], children[0].decode_alignment_as_list_of_sequences())
self.assertEqual(["--M"], children[1].decode_alignment_as_list_of_sequences())
def test_should_get_original_char_position_in_aligned_sequence(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2', 'seq3']
problem.number_of_variables = 3
msa = MSASolution(problem,
msa=[('seq1', '-ABC'), ('seq2', 'ABCD'),
('seq3', '--AB')])
# check
self.assertEqual(
1,
msa.get_original_char_position_in_aligned_sequence(seq_index=0,
position=0))
self.assertEqual(
2,
msa.get_original_char_position_in_aligned_sequence(seq_index=0,
position=1))
self.assertEqual(
3,
msa.get_original_char_position_in_aligned_sequence(seq_index=0,
position=2))
self.assertEqual(
0,
msa.get_original_char_position_in_aligned_sequence(seq_index=1,
position=0))
self.assertEqual(
1,
msa.get_original_char_position_in_aligned_sequence(seq_index=1,
position=1))
self.assertEqual(
2,
msa.get_original_char_position_in_aligned_sequence(seq_index=1,
position=2))
self.assertEqual(
2,
msa.get_original_char_position_in_aligned_sequence(seq_index=2,
position=0))
self.assertEqual(
3,
msa.get_original_char_position_in_aligned_sequence(seq_index=2,
position=1))
def test_should_single_point_crossover_work_properly_case_f(self, random_call):
""" GKGD---P|KK, GKGD-P|KK => GKGD---PKK, GKGD-P-KK
M------Q|DR-, --M--Q|DR => M------QDR, --M--QDR- """
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2']
problem.number_of_variables = 2
msa_1 = MSASolution(problem, msa=[('seq1', 'GKGD---PKK'), ('seq2', 'M------QDR-')])
msa_2 = MSASolution(problem, msa=[('seq1', 'GKGD-PKK'), ('seq2', '--M--QDR')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
random_call.return_value = 7
children = crossover.execute([msa_1, msa_2])
# check
self.assertEqual(["GKGD---PKK", "M------QDR"], children[0].decode_alignment_as_list_of_sequences())
self.assertEqual(["GKGD-P-KK", "--M--QDR-"], children[1].decode_alignment_as_list_of_sequences())
def test_should_single_point_crossover_work_properly_case_a_with_remove_gap_columns(self, random_call):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1']
problem.number_of_variables = 1
msa_1 = MSASolution(problem, msa=[('seq1', 'AB--CD-E')])
msa_2 = MSASolution(problem, msa=[('seq1', 'AB--CDE-')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
crossover_remove_full = SPXMSA(probability=1.0, remove_gap_columns=True)
# run
random_call.return_value = 4
children_1 = crossover.execute([msa_1, msa_2])
children_2 = crossover_remove_full.execute([msa_1, msa_2])
# check
self.assertEqual(["AB--CDE-"], children_1[0].decode_alignment_as_list_of_sequences())
self.assertEqual(["AB--CD-E"], children_1[1].decode_alignment_as_list_of_sequences())
self.assertEqual(["ABCDE"], children_2[0].decode_alignment_as_list_of_sequences())
self.assertEqual(["ABCDE"], children_2[1].decode_alignment_as_list_of_sequences())
def __find_original_positions_in_aligned_sequences(
self, solution: MSASolution,
column_positions_in_first_parent: list):
positions = [-1 for _ in range(solution.number_of_variables)]
for i in range(solution.number_of_variables):
pos = column_positions_in_first_parent[i]
positions[
i] = solution.get_original_char_position_in_aligned_sequence(
i, pos)
return positions
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 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 test_should_find_max_sequence_length(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['a', 'b', 'c']
problem.number_of_variables = 3
msa = MSASolution(problem, msa=[('a', 'AAC'), ('b', 'AAAAAAAC'), ('c', 'C')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
max = crossover.find_length_of_the_largest_sequence(msa)
# check
self.assertEqual(8, max)
def test_should_fill_sequences_with_gaps_to_reach_the_max_sequence_length(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['a', 'b']
problem.number_of_variables = 2
msa_1 = MSASolution(problem, msa=[('a', '-----GE'), ('b', 'KWPFFQEAQK')])
msa_2 = MSASolution(problem, msa=[('a', '-----GE'), ('b', 'KWPFFQEAQK')])
msa_3 = MSASolution(problem, msa=[('a', '-'), ('b', 'ABC')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
crossover.fill_sequences_with_gaps_to_reach_the_max_sequence_length(msa_1, 10, [-1, -1])
crossover.fill_sequences_with_gaps_to_reach_the_max_sequence_length(msa_2, 10, [-1, 5])
crossover.fill_sequences_with_gaps_to_reach_the_max_sequence_length(msa_3, 5, [-1, 1])
# check
self.assertEqual(["-----G---E", "KWPFFQEAQK"], msa_1.decode_alignment_as_list_of_sequences())
self.assertEqual(["-----G---E", "KWPFFQEAQK"], msa_2.decode_alignment_as_list_of_sequences())
self.assertEqual(["-----", "AB--C"], msa_3.decode_alignment_as_list_of_sequences())
def test_should_find_original_positions_in_solution_with_gaps(self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2']
problem.number_of_variables = 2
msa = MSASolution(problem, msa=[('seq1', 'BC-D-E---'), ('seq2', '--C--E---')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
cutting_points = crossover.find_original_positions_in_original_sequences(msa, 5)
# check
self.assertEqual(3, cutting_points[0])
self.assertEqual(1, cutting_points[1])