def test_statistics_samples_datasetsnotexists(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
datasets = 'dataset.txt'
s.compute_statistics = MagicMock()
s.statistics_samples(samples, datasets)
s.compute_statistics.assert_called_once_with(
['POLR2A', 'ASDURF', 'POLR1C'], [], 'statistics.txt')
def test_statistics_samples_parameters(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
sample_pandas = ['samples-pandas']
datasets = Path(__file__).parent.joinpath('dataset.txt')
datasets_pandas = ['datasets-pandas']
output = 'out.txt'
s.compute_statistics = MagicMock()
s.statistics_samples(samples, datasets, output)
s.compute_statistics.assert_called_once_with(
['POLR2A', 'ASDURF', 'POLR1C'], ['POLR2A', 'ASDURF', 'POLR1C'], output)
def test_headers_missmatch(testdir, mock_testclass):
samples = ['POLR2A', 'ASDURF']
datasets = ['POLR1C']
sample1_headers = [
samples[0] + '-100-110', samples[0] + '-110-120',
samples[0] + '-130-140'
]
sample2_headers = [
samples[1] + '-100-110', samples[1] + '-110-120',
samples[1] + '-130-140'
]
dataset1_headers = [
datasets[0] + '-100-110', datasets[0] + '-120-130',
datasets[0] + '-140-150'
]
Split.splits = MagicMock(
side_effect=[sample1_headers, sample2_headers, dataset1_headers])
headers, splits_headers = s.headers(samples, datasets)
assert headers[0] == 'Sample'
assert headers[1] == 'Total reads'
assert headers[2] == 'Mapped reads'
assert headers[3] == 'Deduplicated reads'
assert headers[4] == '100-110'
assert headers[5] == '110-120'
assert headers[6] == '120-130'
assert headers[7] == '130-140'
assert headers[8] == '140-150'
assert len(headers) == 9
assert splits_headers[0] == '100-110'
assert splits_headers[1] == '110-120'
assert splits_headers[2] == '120-130'
assert splits_headers[3] == '130-140'
assert splits_headers[4] == '140-150'
assert len(splits_headers) == 5
def test_flagstat_total_2(testdir, mock_testclass):
bam = 'POLR2A.bam'
output = MagicMock()
output.stdout = MagicMock()
output.stdout.decode = MagicMock(return_value='200')
subprocess.run = MagicMock(return_value=output)
total = s.flagstat_total(bam)
subprocess.run.assert_any_call(['samtools', 'flagstat', bam],
capture_output=True,
check=True)
assert total == '200'
def test_sample_statistics_notexists(testdir, mock_testclass):
sample = 'POLR2A'
splits = ['100-110', '120-130']
s.flagstat_total = MagicMock(side_effect=[300, 200])
Bed.count_bed = MagicMock(side_effect=[150, 50, 40])
stats = s.sample_statistics(sample, splits)
assert stats[0] == sample
assert stats[1] == ''
assert stats[2] == ''
assert stats[3] == ''
assert stats[4] == ''
assert stats[5] == ''
assert len(stats) == 6
s.flagstat_total.assert_not_called()
Bed.count_bed.assert_not_called()
def test_compute_statistics(testdir, mock_testclass):
samples = ['POLR2A', 'ASDURF']
datasets = ['POLR1C']
output = 'out.txt'
splits = ['100-110', '120-130']
s.headers = MagicMock(return_value=([
'Sample', 'Total reads', 'Mapped reads', 'Deduplicated reads',
'100-110', '120-130'
], splits))
s.sample_statistics = MagicMock(side_effect=[[
'POLR2A', 500, 400, 300, 60, 40
], ['ASDURF', 550, 450, 350, 70, 50], ['POLR1C', '', '', 250, 50, 30]])
s.compute_statistics(samples, datasets, output)
s.headers.assert_called_once_with(samples, datasets)
s.sample_statistics.assert_any_call(samples[0], splits)
s.sample_statistics.assert_any_call(samples[1], splits)
s.sample_statistics.assert_any_call(datasets[0], splits)
with open(output, 'r') as infile:
assert infile.readline(
) == 'Sample\tTotal reads\tMapped reads\tDeduplicated reads\t100-110\t120-130\n'
assert infile.readline() == 'POLR2A\t500\t400\t300\t60\t40\n'
assert infile.readline() == 'ASDURF\t550\t450\t350\t70\t50\n'
assert infile.readline() == 'POLR1C\t\t\t250\t50\t30\n'
assert infile.readline() == ''
def test_headers(testdir, mock_testclass):
samples = ['POLR2A', 'ASDURF']
datasets = ['POLR1C']
Split.splits = MagicMock(side_effect=splits)
headers, splits_headers = s.headers(samples, datasets)
assert headers[0] == 'Sample'
assert headers[1] == 'Total reads'
assert headers[2] == 'Mapped reads'
assert headers[3] == 'Deduplicated reads'
assert headers[4] == '100-110'
assert headers[5] == '110-120'
assert headers[6] == '120-140'
assert len(headers) == 7
assert splits_headers[0] == '100-110'
assert splits_headers[1] == '110-120'
assert splits_headers[2] == '120-140'
assert len(splits_headers) == 3
def test_sample_statistics(testdir, mock_testclass):
sample = 'POLR2A'
Path(sample + '.bam').touch()
Path(sample + '-filtered.bam').touch()
Path(sample + '.bed').touch()
splits = ['100-110', '120-130']
for split in splits:
Path(sample + '-' + split + '.bed').touch()
s.flagstat_total = MagicMock(side_effect=[300, 200])
Bed.count_bed = MagicMock(side_effect=[150, 50, 40])
stats = s.sample_statistics(sample, splits)
assert stats[0] == sample
assert stats[1] == 300
assert stats[2] == 200
assert stats[3] == 150 * 2
assert stats[4] == 50
assert stats[5] == 40
assert len(stats) == 6
s.flagstat_total.assert_any_call(sample + '.bam')
s.flagstat_total.assert_any_call(sample + '-filtered.bam')
Bed.count_bed.assert_any_call(sample + '.bed')
Bed.count_bed.assert_any_call(sample + '-100-110.bed')
Bed.count_bed.assert_any_call(sample + '-120-130.bed')