def test_create_heatmap(testdir, mock_testclass):
sample = 'POLR2A'
genes = [
'YDR524W-C', 'YLR355C', 'YLR110C', 'YGR192C', 'YGL008C', 'YKL060C'
]
splits = ['POLR2A-100-110', 'POLR2A-120-130']
splits_values = {}
for split in splits:
splits_values[split] = {}
for gene in genes:
splits_values[split][gene] = str(random.random())
output = 'out.txt'
v.create_heatmap(sample, genes, splits, splits_values, output)
with open(output, 'r') as infile:
assert infile.readline() == 'UNIQID\tName\t100-110\t120-130\n'
assert infile.readline() == 'EWEIGHT\t\t1\t1\n'
assert infile.readline() == 'YDR524W-C\tYDR524W-C\t' + splits_values[
'POLR2A-100-110']['YDR524W-C'] + '\t' + splits_values[
'POLR2A-120-130']['YDR524W-C'] + '\n'
assert infile.readline() == 'YLR355C\tYLR355C\t' + splits_values[
'POLR2A-100-110']['YLR355C'] + '\t' + splits_values[
'POLR2A-120-130']['YLR355C'] + '\n'
assert infile.readline() == 'YLR110C\tYLR110C\t' + splits_values[
'POLR2A-100-110']['YLR110C'] + '\t' + splits_values[
'POLR2A-120-130']['YLR110C'] + '\n'
assert infile.readline() == 'YGR192C\tYGR192C\t' + splits_values[
'POLR2A-100-110']['YGR192C'] + '\t' + splits_values[
'POLR2A-120-130']['YGR192C'] + '\n'
assert infile.readline() == 'YGL008C\tYGL008C\t' + splits_values[
'POLR2A-100-110']['YGL008C'] + '\t' + splits_values[
'POLR2A-120-130']['YGL008C'] + '\n'
assert infile.readline() == 'YKL060C\tYKL060C\t' + splits_values[
'POLR2A-100-110']['YKL060C'] + '\t' + splits_values[
'POLR2A-120-130']['YKL060C'] + '\n'
assert infile.readline() == ''
def test_create_parameters_selection(testdir, mock_testclass):
parameters = Path(__file__).parent.joinpath('parameters.txt')
selection = Path(__file__).parent.joinpath('selection.txt')
beds = ['POLR2A-100-110.bed', 'POLR2A-120-130.bed']
output_folder = 'output'
parameters_output = 'params-out.txt'
v.create_parameters(beds, output_folder, selection, parameters,
parameters_output)
with open(parameters, 'r') as expectedfile, open(parameters_output,
'r') as actualfile:
expected = expectedfile.readline()
while expected != '':
if expected.startswith('~~@dataset_path='):
for bed in beds:
assert '~~@dataset_path=R1:=:' + bed + '\n' == actualfile.readline(
)
elif expected.startswith('~~@output_directory='):
assert '~~@output_directory=' + output_folder + '\n' == actualfile.readline(
)
elif expected.startswith('~~@prefix_filename='):
assert '~~@prefix_filename=\n' == actualfile.readline()
elif expected.startswith('~~@selection_path='):
assert '~~@selection_path=' + str(
selection) + '\n' == actualfile.readline()
else:
assert expected == actualfile.readline()
expected = expectedfile.readline()
assert actualfile.readline() == ''
def test_vap_samples_second(testdir, mock_testclass):
samples_file = Path(__file__).parent.joinpath('samples.txt')
samples = ['POLR2A', 'ASDURF', 'POLR1C']
Parser.first = MagicMock(return_value=samples)
v.vap_sample = MagicMock()
v.vap_samples(samples_file, index=1)
v.vap_sample.assert_any_call(samples[1], 'parameters.txt', None)
Parser.first.assert_called_once_with(samples_file)
def test_vap_samples_second_parameters(testdir, mock_testclass):
samples_file = Path(__file__).parent.joinpath('samples.txt')
parameters = Path(__file__).parent.joinpath('parameters.txt')
selection = Path(__file__).parent.joinpath('genes.txt')
samples = ['POLR2A', 'ASDURF', 'POLR1C']
Parser.first = MagicMock(return_value=samples)
v.vap_sample = MagicMock()
v.vap_samples(samples_file, parameters, selection, 1)
v.vap_sample.assert_any_call(samples[1], parameters, selection)
Parser.first.assert_called_once_with(samples_file)
def test_parse_heatmap_values(testdir, mock_testclass):
sample_splits = ['POLR2A-100-110', 'POLR2A-120-130']
output_folder = str(testdir)
copyfile(
Path(__file__).parent.joinpath('ind_data_POLR2A-100-110.txt'),
'ind_data_POLR2A-100-110.txt')
copyfile(
Path(__file__).parent.joinpath('ind_data_POLR2A-120-130.txt'),
'ind_data_POLR2A-120-130.txt')
heatmap = v.parse_heatmap_values(sample_splits, output_folder)
for split in sample_splits:
assert split in heatmap
assert 'YCR088W' in heatmap['POLR2A-100-110']
assert heatmap['POLR2A-100-110']['YCR088W'] == '1.2'
assert 'YMR282C' in heatmap['POLR2A-100-110']
assert heatmap['POLR2A-100-110']['YMR282C'] == '2.408'
assert 'YOR374W' in heatmap['POLR2A-100-110']
assert heatmap['POLR2A-100-110']['YOR374W'] == '0.34'
assert 'YPR185W' in heatmap['POLR2A-100-110']
assert heatmap['POLR2A-100-110']['YPR185W'] == '0.978'
assert 'YPL259C' in heatmap['POLR2A-100-110']
assert heatmap['POLR2A-100-110']['YPL259C'] == '1.5883'
assert 'YER107C' in heatmap['POLR2A-120-130']
assert heatmap['POLR2A-120-130']['YER107C'] == '1.32'
assert 'YEL056W' in heatmap['POLR2A-120-130']
assert heatmap['POLR2A-120-130']['YEL056W'] == '1.9516'
assert 'YNL037C' in heatmap['POLR2A-120-130']
assert heatmap['POLR2A-120-130']['YNL037C'] == '0'
assert 'YDR017C' in heatmap['POLR2A-120-130']
assert heatmap['POLR2A-120-130']['YDR017C'] == '0.832'
assert 'YKL186C' in heatmap['POLR2A-120-130']
assert heatmap['POLR2A-120-130']['YKL186C'] == '0.224'
def test_parse_genes_selection(testdir, mock_testclass):
parameters = 'parameters_selection.txt'
copyfile(
Path(__file__).parent.joinpath('parameters_selection.txt'), parameters)
copyfile(Path(__file__).parent.joinpath('genes.txt'), 'genes.txt')
selection = Path(__file__).parent.joinpath('selection.txt')
genes = v.parse_genes(parameters, selection)
assert genes[0] == 'YLR110C'
assert genes[1] == 'YGL008C'
def test_vap_sample_parseheatmaperror(testdir, mock_testclass):
sample = 'POLR2A'
parameters = Path(__file__).parent.joinpath('parameters.txt')
selection = Path(__file__).parent.joinpath('genes.txt')
splits = ['POLR2A-100-110', 'POLR2A-120-130']
genes = [
'YDR524W-C', 'YLR355C', 'YLR110C', 'YGR192C', 'YGL008C', 'YKL060C'
]
beds = [split + '-cov.bed' for split in splits]
output = sample + '-vap-output'
sample_parameters = output + '/parameters.txt'
Split.splits = MagicMock(return_value=splits)
v.parse_genes = MagicMock(return_value=genes)
v.create_parameters = MagicMock()
subprocess.run = MagicMock()
v.parse_heatmap_values = MagicMock(side_effect=AssertionError)
v.create_heatmap = MagicMock()
with pytest.raises(AssertionError):
v.vap_sample(sample, parameters, selection)
def test_parse_genes(testdir, mock_testclass):
parameters = 'parameters.txt'
copyfile(Path(__file__).parent.joinpath('parameters.txt'), parameters)
copyfile(Path(__file__).parent.joinpath('genes.txt'), 'genes.txt')
genes = v.parse_genes(parameters)
assert genes[0] == 'YDR524W-C'
assert genes[1] == 'YLR355C'
assert genes[2] == 'YLR110C'
assert genes[3] == 'YGR192C'
assert genes[4] == 'YGL008C'
assert genes[5] == 'YKL060C'
def test_vap_sample(testdir, mock_testclass):
sample = 'POLR2A'
parameters = Path(__file__).parent.joinpath('parameters.txt')
selection = Path(__file__).parent.joinpath('genes.txt')
splits = ['POLR2A-100-110', 'POLR2A-120-130']
genes = [
'YDR524W-C', 'YLR355C', 'YLR110C', 'YGR192C', 'YGL008C', 'YKL060C'
]
beds = [split + '-cov.bed' for split in splits]
output = sample + '-vap-output'
sample_parameters = output + '/parameters.txt'
splits_values = {}
for split in splits:
splits_values[split] = {}
for gene in genes:
splits_values[split][gene] = str(random.random())
merged_heatmap = sample + '-heatmap.txt'
Split.splits = MagicMock(return_value=splits)
v.parse_genes = MagicMock(return_value=genes)
v.create_parameters = MagicMock()
subprocess.run = MagicMock()
v.parse_heatmap_values = MagicMock(return_value=splits_values)
v.create_heatmap = MagicMock()
shutil.rmtree = MagicMock()
v.vap_sample(sample, parameters, selection)
Split.splits.assert_called_once_with(sample)
v.parse_genes.assert_called_once_with(parameters, selection)
v.create_parameters.assert_called_once_with(beds, output, selection,
parameters, sample_parameters)
cmd = ['vap']
if os.name == 'nt':
cmd = ['vap.exe']
cmd.extend(['-p', sample_parameters])
subprocess.run.assert_called_once_with(cmd, check=True)
v.parse_heatmap_values.assert_called_once_with(splits, output)
v.create_heatmap.assert_called_once_with(sample, genes, splits,
splits_values, merged_heatmap)
shutil.rmtree.assert_called_once_with(output)
def test_parse_heatmap_values_noheatmapfiles(testdir, mock_testclass):
sample_splits = ['POLR2A-100-110', 'POLR2A-120-130']
output_folder = str(os.curdir)
with pytest.raises(AssertionError):
v.parse_heatmap_values(sample_splits, output_folder)