def test_split_samples(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
ss.split_sample = MagicMock()
ss.split_samples(samples)
ss.split_sample.assert_any_call('POLR2A', 10, 100, 500)
ss.split_sample.assert_any_call('ASDURF', 10, 100, 500)
ss.split_sample.assert_any_call('POLR1C', 10, 100, 500)
def test_split_sample(testdir, mock_testclass):
sample = 'POLR2A'
bed = sample + '.bed'
ss.filter_bed_by_length = MagicMock()
binlength = 10
binminlength = 100
binmaxlength = 200
ss.split_sample(sample, binlength, binminlength, binmaxlength)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-100-110.bed', 100,
110)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-110-120.bed', 110,
120)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-120-130.bed', 120,
130)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-130-140.bed', 130,
140)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-140-150.bed', 140,
150)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-150-160.bed', 150,
160)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-160-170.bed', 160,
170)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-170-180.bed', 170,
180)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-180-190.bed', 180,
190)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-190-200.bed', 190,
200)
assert ss.filter_bed_by_length.call_count == 10
def test_split_samples_second_parameters(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
ss.split_sample = MagicMock()
binlength = 20
binminlength = 200
binmaxlength = 400
ss.split_samples(samples, 1, binlength, binminlength, binmaxlength)
ss.split_sample.assert_called_once_with('ASDURF', binlength, binminlength,
binmaxlength)
def test_filter_bed_by_length_3(testdir, mock_testclass):
bed = Path(__file__).parent.joinpath('sample-slowsplit.bed')
out = 'out.bed'
bin_start = 100
bin_end = 110
ss.filter_bed_by_length(bed, out, bin_start, bin_end)
with open(out, 'r') as infile:
assert infile.readline() == 'chr4\t800\t900\ttest4\t4\t+\n'
assert infile.readline() == ''
def test_split_sample_largerbin(testdir, mock_testclass):
sample = 'POLR2A'
bed = sample + '.bed'
ss.filter_bed_by_length = MagicMock()
binlength = 100
binminlength = 110
binmaxlength = 190
ss.split_sample(sample, binlength, binminlength, binmaxlength)
ss.filter_bed_by_length.assert_called_once_with(bed,
sample + '-110-190.bed',
110, 190)
def test_split_samples_parameters(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
ss.split_sample = MagicMock()
binlength = 20
binminlength = 200
binmaxlength = 400
ss.split_samples(samples,
binlength=binlength,
binminlength=binminlength,
binmaxlength=binmaxlength)
ss.split_sample.assert_any_call('POLR2A', binlength, binminlength,
binmaxlength)
ss.split_sample.assert_any_call('ASDURF', binlength, binminlength,
binmaxlength)
ss.split_sample.assert_any_call('POLR1C', binlength, binminlength,
binmaxlength)
def test_split_sample_shorterlastbin(testdir, mock_testclass):
sample = 'POLR2A'
bed = sample + '.bed'
ss.filter_bed_by_length = MagicMock()
binlength = 10
binminlength = 155
binmaxlength = 200
ss.split_sample(sample, binlength, binminlength, binmaxlength)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-155-165.bed', 155,
165)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-165-175.bed', 165,
175)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-175-185.bed', 175,
185)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-185-195.bed', 185,
195)
ss.filter_bed_by_length.assert_any_call(bed, sample + '-195-200.bed', 195,
200)
assert ss.filter_bed_by_length.call_count == 5
def test_split_samples_second(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
ss.split_sample = MagicMock()
ss.split_samples(samples, 1)
ss.split_sample.assert_called_once_with('ASDURF', 10, 100, 500)