def test_remove_duplicates_singlethread(testdir, mock_testclass):
bam = 'POLR2A.bam'
output = 'POLR2A-out.bam'
threads = 1
subprocess.run = MagicMock(side_effect=[
create_file, create_file_fixmate, create_file, create_file_markdup,
create_file
])
fb.remove_duplicates(bam, output, threads)
subprocess.run.assert_any_call(['samtools', 'sort', '-n', '-o', ANY, bam],
check=True)
subprocess.run.assert_any_call(['samtools', 'fixmate', '-m', ANY, ANY],
check=True)
subprocess.run.assert_any_call(['samtools', 'sort', '-o', ANY, ANY],
check=True)
subprocess.run.assert_any_call(['samtools', 'markdup', '-r', ANY, ANY],
check=True)
subprocess.run.assert_any_call(['samtools', 'sort', '-o', output, ANY],
check=True)
assert subprocess.run.call_args_list[0].args[0][
4] == subprocess.run.call_args_list[1].args[0][3]
assert subprocess.run.call_args_list[1].args[0][
4] == subprocess.run.call_args_list[2].args[0][4]
assert subprocess.run.call_args_list[2].args[0][
3] == subprocess.run.call_args_list[3].args[0][3]
assert subprocess.run.call_args_list[3].args[0][
4] == subprocess.run.call_args_list[3].args[0][4]
def test_filter_bam(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
fb.filter_bam_sample = MagicMock()
fb.filter_bam(samples)
fb.filter_bam_sample.assert_any_call('POLR2A', True, True, None, '', '')
fb.filter_bam_sample.assert_any_call('ASDURF', True, True, None, '', '')
fb.filter_bam_sample.assert_any_call('POLR1C', True, True, None, '', '')
def test_sort(testdir, mock_testclass):
bam = 'POLR2A.bam'
output = 'POLR2A-out.bam'
subprocess.run = MagicMock()
fb.sort(bam, output)
subprocess.run.assert_any_call(['samtools', 'sort', '-o', output, bam],
check=True)
def test_filter_bam_second(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
threads = 2
fb.filter_bam_sample = MagicMock()
fb.filter_bam(samples, False, True, threads, index=1)
fb.filter_bam_sample.assert_called_once_with('ASDURF', False, True,
threads, '', '')
def test_sort_threads(testdir, mock_testclass):
bam = 'POLR2A.bam'
output = 'POLR2A-out.bam'
threads = 3
subprocess.run = MagicMock()
fb.sort(bam, output, threads)
subprocess.run.assert_any_call(
['samtools', 'sort', '--threads',
str(threads - 1), '-o', output, bam],
check=True)
def test_filter_mapped_paired(testdir, mock_testclass):
bam = 'POLR2A.bam'
output = 'POLR2A-out.bam'
subprocess.run = MagicMock(side_effect=create_file)
fb.filter_mapped(bam, output, True)
subprocess.run.assert_any_call(
['samtools', 'view', '-b', '-F', '2048', '-f', '2', '-o', ANY, bam],
check=True)
subprocess.run.assert_any_call(['samtools', 'sort', '-o', output, ANY],
check=True)
assert subprocess.run.call_args_list[0].args[0][
8] == subprocess.run.call_args_list[1].args[0][4]
def test_filter_bam_sample_paired_nodedup(testdir, mock_testclass):
sample = 'POLR2A'
bam = sample + '.bam'
bam_filtered = sample + '-filtered.bam'
bam_dedup = sample + '-dedup.bam'
fb.filter_mapped = MagicMock(create_file(['-o', bam_filtered]))
fb.remove_duplicates = MagicMock()
fb.filter_bam_sample(sample, True, False)
fb.filter_mapped.assert_called_with(bam, bam_filtered, True, None)
fb.remove_duplicates.assert_not_called()
assert os.path.exists(bam_filtered)
assert not os.path.exists(bam_dedup)
def test_filter_bam_parameters(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
threads = 2
input_suffix = '-i-sacCer'
output_suffix = '-sacCer'
fb.filter_bam_sample = MagicMock()
fb.filter_bam(samples, False, False, threads, input_suffix, output_suffix)
fb.filter_bam_sample.assert_any_call('POLR2A', False, False, threads,
input_suffix, output_suffix)
fb.filter_bam_sample.assert_any_call('ASDURF', False, False, threads,
input_suffix, output_suffix)
fb.filter_bam_sample.assert_any_call('POLR1C', False, False, threads,
input_suffix, output_suffix)
def test_filter_bam_sample_paired_parameters(testdir, mock_testclass):
sample = 'POLR2A'
input_suffix = '-i-sacCer'
output_suffix = '-sacCer'
bam = sample + input_suffix + '.bam'
bam_filtered = sample + output_suffix + '-filtered.bam'
bam_dedup = sample + output_suffix + '-dedup.bam'
threads = 3
fb.filter_mapped = MagicMock(create_file(['-o', bam_filtered]))
fb.remove_duplicates = MagicMock(create_file(['-o', bam_dedup]))
fb.filter_bam_sample(sample, True, True, threads, input_suffix,
output_suffix)
fb.filter_mapped.assert_called_with(bam, bam_filtered, True, threads)
fb.remove_duplicates.assert_called_with(bam_filtered, bam_dedup, threads)
assert os.path.exists(bam_filtered)
assert os.path.exists(bam_dedup)
def test_filter_mapped_single_threads(testdir, mock_testclass):
bam = 'POLR2A.bam'
output = 'POLR2A-out.bam'
threads = 3
subprocess.run = MagicMock(side_effect=create_file)
fb.filter_mapped(bam, output, False, threads)
subprocess.run.assert_any_call([
'samtools', 'view', '-b', '-F', '2048', '-F', '4', '--threads',
str(threads - 1), '-o', ANY, bam
],
check=True)
subprocess.run.assert_any_call(
['samtools', 'sort', '--threads',
str(threads - 1), '-o', output, ANY],
check=True)
assert subprocess.run.call_args_list[0].args[0][
10] == subprocess.run.call_args_list[1].args[0][6]