def test_run_blossum(self):
pairs_to_result = {
('ILDMDVVEGSAARFDCKVEGYPDPEVMWFKDDNPVKESRHFQIDYDEEGN', 'RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFVSQTT'):
0,
('ILDMDVVEGSAARFDCKVEGYPDPEVMWFKDDNPVKESRHFQIDYDEEGN', 'ISDTEADIGSNLRWGCAAAGKPRPMVRWLRNGEPLASQNRVEVLA'):
41,
('ILDMDVVEGSAARFDCKVEGYPDPEVMWFKDDNPVKESRHFQIDYDEEGN', 'RRLIPAARGGEISILCQPRAAPKATILWSKGTEILGNSTRVTVTSD'):
5,
('RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFVSQTT', 'RRLIPAARGGEISILCQPRAAPKATILWSKGTEILGNSTRVTVTSD'):
-4,
('ISDTEADIGSNLRWGCAAAGKPRPMVRWLRNGEPLASQNRVEVLA', 'RRLIPAARGGEISILCQPRAAPKATILWSKGTEILGNSTRVTVTSD'):
18,
('RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFVSQTT', 'ISDTEADIGSNLRWGCAAAGKPRPMVRWLRNGEPLASQNRVEVLA'):
-5
}
sequence_file = '../data/guideline_tests/needlemanwunsch.fa'
sequences = parse_fasta_files([sequence_file])
gt = Gotoh(substitution_matrix=MatrixInfo.blosum62,
gap_penalty=11,
gap_extend=1,
similarity=True,
verbose=False,
complete_traceback=True)
results = gt.pairwise_alignments(sequences)
for result in results:
seqs = (str(result.seq1), str(result.seq2))
expected_score = pairs_to_result[seqs]
self.assertEqual(result.score, expected_score)
print(len(result.alignments))
def test_guideline_blosum():
"""Test cases given on the guideline from 04.02.2019
the results are not as provided by the guideline
"""
gotoh = Gotoh()
result, info = gotoh.run("data/xpgma_guideline.fasta",
"data/xpgma_guideline.fasta",
"data/blosum62.txt",
False,
11,
1,
True)
# the results is a upper triangle matrix of shape n x n.
seq1_seq2 = result[0][1]
assert seq1_seq2[3] == 0
assert len(seq1_seq2[2]) == 1
assert seq1_seq2[2][0] == ('ILDMDVVEGSAARFDCKVEG_YPDPEVMWFKDDNP___VKESRHFQIDYDEEGN',
'RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFV____SQTT')
seq1_seq3 = result[0][2]
assert seq1_seq3[3] == 41
assert len(seq1_seq3[2]) == 3
assert seq1_seq3[2][0] == ('ILDMDVVEGSAARFDCKVEGYPDPEVMWFKDDNPVKESRHFQIDYDEEGN',
'ISDTEADIGSNLRWGCAAAGKPRPMVRWLRNGEPLASQNRVEV_____LA')
seq1_seq4 = result[0][3]
assert seq1_seq4[3] == 5
assert len(seq1_seq4[2]) == 1
assert seq1_seq4[2][0] == ('ILDMDVVEGSAARFDCKVEGYPDPEVMWFKDDNPVKESRHFQIDYDEEGN',
'RRLIPAARGGEISILCQPRAAPKATILWSKGTEILGNSTRVTVTSD____')
seq2_seq3 = result[1][2]
assert seq2_seq3[3] == -5
assert len(seq2_seq3[2]) == 4
assert seq2_seq3[2][0] == ('RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFVSQTT',
'ISDTEADIGSNLRWGC_AAAGKPRPMVRWLRNG____EPLASQNRVEVLA')
seq2_seq4 = result[1][3]
assert seq2_seq4[3] == -4
assert len(seq2_seq4[2]) == 2
assert seq2_seq4[2][0] == ('RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFVSQTT',
'RRLIPAARGGEISILCQPRA_APKATILW__SKGTEILGNSTRVTVT_SD')
seq3_seq4 = result[2][3]
assert seq3_seq4[3] == 18
assert len(seq3_seq4[2]) == 1
assert seq3_seq4[2][0] == ('ISDTEADIGSNLRWGCAAAGKPRPMVRWLRNGEPLASQNRVEVLA_',
'RRLIPAARGGEISILCQPRAAPKATILWSKGTEILGNSTRVTVTSD')
def test_example_invalid_characters_fail():
"""This function does a negative test: it checks if it fails when it is supposed to.
The reason for failure is non-amino acid characters in file 2 (error code 12)"""
gt = Gotoh()
seq_fasta_1 = os.path.join('data','sequences','seq1.fasta')
seq_fasta_2 = os.path.join('data','sequences','Invalid_characters.fasta')
with pytest.raises(SystemExit) as InvalidCharactersException:
result = gt.run(seq_fasta_1,
seq_fasta_2,
'pam250',
-11,
-1,
False)
(id_seq1, seq1, id_seq2, seq2, score, alignments, num_alignments) = result
assert InvalidCharactersException.type == SystemExit
assert InvalidCharactersException.code == 12
def test_example_invalid_format_fail():
"""This function does a negative test: it checks if it fails when it is supposed to.
The reason for the failure is invalid file format: the first line does not start with >"""
gt = Gotoh()
seq_fasta_1 = os.path.join('data','sequences','seq1.fasta')
seq_fasta_2 = os.path.join('data','sequences','Invalid_format.fasta')
with pytest.raises(SystemExit) as InvalidFileException:
result = gt.run(seq_fasta_2,
seq_fasta_1,
'pam250',
-11,
-1,
False)
(id_seq1, seq1, id_seq2, seq2, score, alignments, num_alignments) = result
assert InvalidFileException.type == SystemExit
assert InvalidFileException.code == 1
def test_example():
"""Test if run function can be called."""
gt = Gotoh()
result = gt.run("data/sequence1.fa",
"data/sequence2.fa",
"data/blosum62.txt",
5,
20,
False)
(id_seq1, seq1, id_seq2, seq2, score, alignments) = result
assert id_seq1 == "idA"
assert id_seq2 == "idB"
assert seq1 == "FancySequenceA"
assert seq2 == "FancysequenceB"
assert score == 1000
assert alignments[0] == ("Fancy_SequenceA_",
"Fancys_equence_B")
def test_example():
"""Test if run function can be called."""
gt = Gotoh()
result, info = gt.run("data/sequence1.fasta",
"data/sequence2.fasta",
"data/test_scoring_similarity.txt",
False,
5,
1,
True)
assert result[0][0][0].id == "idA"
assert result[0][0][1].id == "idB"
assert str(result[0][0][0].seq) == "TCCGA"
assert str(result[0][0][1].seq) == "TACGCAGA"
assert result[0][0][3] == -4
assert len(result[0][0][2]) == 3
assert result[0][0][2][0] == ('T___CCGA', 'TACGCAGA')
def test_too_few_arguments():
"""This function does a negative test: it checks if it fails when it is supposed to.
The reason for failure is non-amino acid characters in file 2 (error code 12)"""
gt = Gotoh()
seq_fasta_1 = os.path.join('data','sequences','seq1.fasta')
seq_fasta_2 = os.path.join('data','sequences','seq2.fasta')
# test is a variable which becomes True when there are too few arguments
test = False
try:
with pytest.raises(SystemExit) as TooFewArguments:
result = gt.run(seq_fasta_1,
seq_fasta_2,
'pam250',
-1,
False)
(id_seq1, seq1, id_seq2, seq2, score, alignments, num_alignments) = result
# A TypeError is thrown when there are too few arguments (we are missing 1 argument)
except TypeError:
test = True
assert test == True
def test_init(self):
got = Gotoh()
got.init_scoring_matrices("AAAC", "AAAC")
print(got.scoring_matrix_D)
print(got.scoring_matrix_P)
print(got.scoring_matrix_Q)
assert np.array_equal(
got.scoring_matrix_D,
np.array([[0., -12., -13., -14., -15.], [-12., 0., 0., 0., 0.],
[-13., 0., 0., 0., 0.], [-14., 0., 0., 0., 0.],
[-15., 0., 0., 0., 0.]]))
assert np.array_equal(
got.scoring_matrix_P,
np.array([[-math.inf, -math.inf, -math.inf, -math.inf, -math.inf],
[-math.inf, 0., 0., 0., 0.], [-math.inf, 0., 0., 0., 0.],
[-math.inf, 0., 0., 0., 0.], [-math.inf, 0., 0., 0.,
0.]]))
assert np.array_equal(
got.scoring_matrix_Q,
np.array([[-math.inf, -math.inf, -math.inf, -math.inf, -math.inf],
[-math.inf, 0., 0., 0., 0.], [-math.inf, 0., 0., 0., 0.],
[-math.inf, 0., 0., 0., 0.], [-math.inf, 0., 0., 0.,
0.]]))
def test_example_success():
"""This calls the run method of the Needleman-Wunsch program
and tests if it works as expected (positive test)"""
gt = Gotoh()
seq_fasta_1 = os.path.join('data','sequences','seq1.fasta')
seq_fasta_2 = os.path.join('data','sequences','seq2.fasta')
seq_fasta_3 = os.path.join('data','sequences','seq3.fasta')
result = gt.run(seq_fasta_1,
seq_fasta_2,
'pam250',
-11,
-1,
True)
(id_seq1, seq1, id_seq2, seq2, score, alignments,num_alignments) = result
assert id_seq1 == "ID1"
assert id_seq2 == "ID2"
assert seq1 == "ILDMDVVEGSAARFDCKVEGYPDPEVMWFKDDNPVKESRHFQIDYDEEGN"
assert seq2 == "RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFVSQTT"
assert score == 33
assert alignments== [['ILDMDVVEGSAARFDCKVEG-YPDPEVMWFKDDNP---VKESRHFQIDYDEEGN',
'RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFV----SQTT', ':::::::**::::::*:::: **:::::*:::::* ::::***: ::::'], ['ILDMDVVEGSAARFDCKVEG-YPDPEVMWFKDDNP---VKESRHFQIDYDEEGN', 'RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHF----VSQTT', ':::::::**::::::*:::: **:::::*:::::* ::::*** :::::']]
assert num_alignments == 2
def test_scoring_blossum(self):
"""Testing score calculation using Blossum62 + Gap Penalty = -11, gap extend = -1"""
print("######### Testing calculation of scoring matrix. ###########")
got = Gotoh(substitution_matrix=MatrixInfo.blosum62,
gap_penalty=-11,
gap_extend=-1)
print("############# Case 1 ##############")
print("############# START ##############")
seq1 = "A"
seq2 = "A"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % got.scoring_matrix_D)
np.testing.assert_array_equal(got.scoring_matrix_D,
np.array([[0., -12.0], [-12., 4.]]))
print("############# FINISH ##############")
print("############# Case 2 ##############")
print("############# START ##############")
seq1 = "A"
seq2 = "AT"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % got.scoring_matrix_D)
np.testing.assert_array_equal(
got.scoring_matrix_D, np.array([[0., -12., -13.], [-12., 4.,
-8.]]))
print("############# FINISH ##############")
print("############# Case 3 ##############")
print("############# START ##############")
seq1 = "RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFVSQTT"
seq2 = "ISDTEADIGSNLRWGCAAAGKPRPMVRWLRNGEPLASQNRVEVLA"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % pprint.pformat(got.scoring_matrix_D))
self.assertAlmostEqual(got.scoring_matrix_D[-1][-1], -5.0)
print("############# FINISH ##############")
def test_scoring_pam(self):
"""Testing score calculation using PAM250 + Gap Penalty = -11, gap extend = -1"""
print("######### Testing calculation of scoring matrix. ###########")
got = Gotoh(substitution_matrix=MatrixInfo.pam250,
gap_penalty=-11,
gap_extend=-1)
print("############# Case 1 ##############")
print("############# START ##############")
seq1 = "A"
seq2 = "A"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % got.scoring_matrix_D)
np.testing.assert_array_equal(got.scoring_matrix_D,
np.array([[0., -12.], [-12., 2.]]))
print("############# FINISH ##############")
print("############# Case 2 ##############")
print("############# START ##############")
seq1 = "A"
seq2 = "AT"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % got.scoring_matrix_D)
np.testing.assert_array_equal(
got.scoring_matrix_D, np.array([[0., -12., -13.], [-12., 2.,
-10.]]))
print("############# FINISH ##############")
print("############# Case 3 ##############")
print("############# START ##############")
seq1 = "ILDMDVVEGSAARFDCKVEGYPDPEVMWFKDDNPVKESRHFQIDYDEEGN"
seq2 = "RDPVKTHEGWGVMLPCNPPAHYPGLSYRWLLNEFPNFIPTDGRHFVSQTT"
got.calculate_scoring_matrix(seq1, seq2)
print("SEQ1: %s" % seq1)
print("SEQ2: %s" % seq2)
print("RESULT:\n %s" % pprint.pformat(got.scoring_matrix_D))
self.assertAlmostEqual(got.scoring_matrix_D[-1][-1], 33)
print("############# FINISH ##############")
def let_compute(self, input):
"""
Starts the algorithm with the right input parameters.
Args:
input: console input
"""
algorithm = input[0]
if algorithm == available_algorithms.GOTOH:
procedure = Gotoh()
elif algorithm == available_algorithms.NEEDLEMAN_WUNSCH:
procedure = NeedlemanWunsch()
elif algorithm == available_algorithms.NEEDLEMAN_WUNSCH_3D:
procedure = NeedlemanWunsch3()
elif algorithm == available_algorithms.NUSSINOV:
procedure = Nussinov()
procedure.compute(input)
def test_instance():
"""Check inheritance."""
assert issubclass(Gotoh, GotohBase)
assert isinstance(Gotoh(), GotohBase)
