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 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 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_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])
def test_should_find_the_cutting_points_in_the_first_parent_return_minus_one_if_the_point_is_in_a_gap_group_ending_the_sequence(
self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2']
problem.number_of_variables = 2
msa = MSASolution(problem, msa=[('seq1', 'BC-D-E--'), ('seq2', 'ABC-E---')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
cutting_points = crossover.find_cutting_points_in_first_parent(msa, 6)
# check
self.assertEqual([-1, -1], cutting_points)
def test_should_find_the_cutting_points_in_the_first_parent_return_the_column_position_if_it_is_occupied_by_gap(
self):
# setup
problem = MSA(score_list=[])
problem.identifiers = ['seq1', 'seq2']
problem.number_of_variables = 2
msa = MSASolution(problem, msa=[('seq1', 'BC-DE'), ('seq2', 'ABC-E')])
crossover = SPXMSA(probability=1.0, remove_gap_columns=False)
# run
cutting_points = crossover.find_cutting_points_in_first_parent(msa, 2)
# check
self.assertEqual(3, cutting_points[0])
self.assertEqual(2, cutting_points[1])
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_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_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_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_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_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_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())