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_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)