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_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