def test_genome_coverage_samples_second_scale(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
genome = Path(__file__).parent.joinpath('sizes.txt')
scale = 1.5
gc.sample_splits_genome_coverage = MagicMock()
gc.genome_coverage_samples(samples, genome, scale=scale, index=1)
gc.sample_splits_genome_coverage.assert_called_once_with('ASDURF', genome, scale, None, '', '-cov', None, None, ())
def test_genome_coverage_samples_all_three(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
genome = Path(__file__).parent.joinpath('sizes.txt')
gc.sample_splits_genome_coverage = MagicMock()
gc.genome_coverage_samples(samples, genome, genomecov_args=('-3',))
gc.sample_splits_genome_coverage.assert_any_call('POLR2A', genome, None, None, '', '-cov', None, None, ('-3',))
gc.sample_splits_genome_coverage.assert_any_call('ASDURF', genome, None, None, '', '-cov', None, None, ('-3',))
gc.sample_splits_genome_coverage.assert_any_call('POLR1C', genome, None, None, '', '-cov', None, None, ('-3',))
def test_genome_coverage_samples(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
genome = 'sacCer3.chrom.sizes'
copyfile(Path(__file__).parent.joinpath('sizes.txt'), genome)
gc.sample_splits_genome_coverage = MagicMock()
gc.genome_coverage_samples(samples)
gc.sample_splits_genome_coverage.assert_any_call('POLR2A', genome, None, None, '', '-cov', None, None, ())
gc.sample_splits_genome_coverage.assert_any_call('ASDURF', genome, None, None, '', '-cov', None, None, ())
gc.sample_splits_genome_coverage.assert_any_call('POLR1C', genome, None, None, '', '-cov', None, None, ())
def test_genome_coverage_samples_all_scale_positivestrand(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
genome = Path(__file__).parent.joinpath('sizes.txt')
scale = 1.5
strand = '+'
gc.sample_splits_genome_coverage = MagicMock()
gc.genome_coverage_samples(samples, genome, scale=scale, strand=strand)
gc.sample_splits_genome_coverage.assert_any_call('POLR2A', genome, scale, strand, '', '-cov', None, None, ())
gc.sample_splits_genome_coverage.assert_any_call('ASDURF', genome, scale, strand, '', '-cov', None, None, ())
gc.sample_splits_genome_coverage.assert_any_call('POLR1C', genome, scale, strand, '', '-cov', None, None, ())
def test_sample_splits_genome_coverage_three(testdir, mock_testclass):
sample = 'POLR2A'
genome = 'human.sizes'
split1 = sample + '-100-110'
split2 = sample + '-110-120'
sb.splits = MagicMock(return_value=[split1, split2])
gc.genome_coverage = MagicMock()
gc.sample_splits_genome_coverage(sample, genome, genomecov_args=('-3'))
sb.splits.assert_called_once_with(sample)
gc.genome_coverage.assert_any_call(sample, genome, None, None, '', '-cov', None, None, ('-3'))
gc.genome_coverage.assert_any_call(split1, genome, None, None, '', '-cov', None, None, ('-3'))
gc.genome_coverage.assert_any_call(split2, genome, None, None, '', '-cov', None, None, ('-3'))
def test_coverage_three(testdir, mock_testclass):
sample = 'POLR2A'
bed = sample + '.bed'
output = sample + '-out.bed'
genome = 'human.sizes'
subprocess.run = MagicMock(side_effect=create_file)
Bed.sort = MagicMock(side_effect=create_file_sort)
gc.coverage(bed, output, genome, sample, genomecov_args=('-3',))
subprocess.run.assert_called_once_with(['bedtools', 'genomecov', '-bg', '-i', bed, '-g', genome, '-3'], stdout=ANY, check=True)
Bed.sort.assert_called_once_with(ANY, ANY)
with open(output, 'r') as infile:
assert infile.readline() == 'track type=bedGraph name="' + sample + '"\n'
assert infile.readline() == 'test'
def test_sample_splits_genome_coverage_positivestrand(testdir, mock_testclass):
sample = 'POLR2A'
genome = 'human.sizes'
split1 = sample + '-100-110'
split2 = sample + '-110-120'
strand = '+'
sb.splits = MagicMock(return_value=[split1, split2])
gc.genome_coverage = MagicMock()
gc.sample_splits_genome_coverage(sample, genome, strand=strand)
sb.splits.assert_called_once_with(sample)
gc.genome_coverage.assert_any_call(sample, genome, None, strand, '', '-cov', None, None, ())
gc.genome_coverage.assert_any_call(split1, genome, None, strand, '', '-cov', None, None, ())
gc.genome_coverage.assert_any_call(split2, genome, None, strand, '', '-cov', None, None, ())
def test_genome_coverage_scale(testdir, mock_testclass):
sample = 'POLR2A'
bed = sample + '.bed'
cov = sample + '-cov.bed'
bw = sample + '-cov.bw'
genome = 'human.sizes'
scale = 1.5
Bed.count_bed = MagicMock()
gc.coverage = MagicMock()
Bed.bedgraph_to_bigwig = MagicMock()
gc.genome_coverage(sample, genome, scale=scale)
Bed.count_bed.assert_not_called()
gc.coverage.assert_called_once_with(bed, cov, genome, sample, scale, None, ())
Bed.bedgraph_to_bigwig.assert_called_once_with(cov, bw, genome)
def test_genome_coverage_three(testdir, mock_testclass):
sample = 'POLR2A'
bed = sample + '.bed'
cov = sample + '-cov.bed'
bw = sample + '-cov.bw'
genome = 'human.sizes'
count = 2000000
Bed.count_bed = MagicMock(return_value=count)
gc.coverage = MagicMock()
Bed.bedgraph_to_bigwig = MagicMock()
gc.genome_coverage(sample, genome, genomecov_args=('-3'))
Bed.count_bed.assert_called_once_with(bed)
gc.coverage.assert_called_once_with(bed, cov, genome, sample, BASE_SCALE / count, None, ('-3'))
Bed.bedgraph_to_bigwig.assert_called_once_with(cov, bw, genome)
def test_genome_coverage_positivestrand(testdir, mock_testclass):
sample = 'POLR2A'
bed = sample + '.bed'
cov = sample + '-cov-pos.bed'
bw = sample + '-cov-pos.bw'
genome = 'human.sizes'
strand = '+'
count = 2000000
Bed.count_bed = MagicMock(return_value=count)
gc.coverage = MagicMock()
Bed.bedgraph_to_bigwig = MagicMock()
gc.genome_coverage(sample, genome, scale=None, strand=strand)
Bed.count_bed.assert_called_once_with(bed)
gc.coverage.assert_called_once_with(bed, cov, genome, sample, BASE_SCALE / count, strand, ())
Bed.bedgraph_to_bigwig.assert_called_once_with(cov, bw, genome)
def test_genome_coverage_samples_parameters(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
genome = 'sacCer3.chrom.sizes'
copyfile(Path(__file__).parent.joinpath('sizes.txt'), genome)
scale = 1.5
strand = '+'
input_suffix = '-forcov'
output_suffix = '-outcov'
spike_suffix = '-pombe'
control_suffix = '-input'
gc.sample_splits_genome_coverage = MagicMock()
gc.genome_coverage_samples(samples, genome, scale, strand, input_suffix, output_suffix, spike_suffix, control_suffix, genomecov_args=('-5',))
gc.sample_splits_genome_coverage.assert_any_call('POLR2A', genome, scale, strand, input_suffix, output_suffix, spike_suffix, control_suffix, ('-5',))
gc.sample_splits_genome_coverage.assert_any_call('ASDURF', genome, scale, strand, input_suffix, output_suffix, spike_suffix, control_suffix, ('-5',))
gc.sample_splits_genome_coverage.assert_any_call('POLR1C', genome, scale, strand, input_suffix, output_suffix, spike_suffix, control_suffix, ('-5',))
def test_genome_coverage_suffix(testdir, mock_testclass):
sample = 'POLR2A'
input_suffix = '-forcov'
output_suffix = '-outcov'
bed = sample + input_suffix + '.bed'
cov = sample + output_suffix + '.bed'
bw = sample + output_suffix + '.bw'
genome = 'human.sizes'
count = 2000000
Bed.count_bed = MagicMock(return_value=count)
gc.coverage = MagicMock()
Bed.bedgraph_to_bigwig = MagicMock()
gc.genome_coverage(sample, genome, input_suffix=input_suffix, output_suffix=output_suffix)
Bed.count_bed.assert_called_once_with(bed)
gc.coverage.assert_called_once_with(bed, cov, genome, sample, BASE_SCALE / count, None, ())
Bed.bedgraph_to_bigwig.assert_called_once_with(cov, bw, genome)
def test_sample_splits_genome_coverage_parameters(testdir, mock_testclass):
sample = 'POLR2A'
genome = 'human.sizes'
split1 = sample + '-100-110'
split2 = sample + '-110-120'
scale = 1.5
strand = '+'
input_suffix = '-forcov'
output_suffix = '-outcov'
spike_suffix = '-pombe'
control_suffix = '-input'
sb.splits = MagicMock(return_value=[split1, split2])
gc.genome_coverage = MagicMock()
gc.sample_splits_genome_coverage(sample, genome, scale, strand, input_suffix, output_suffix, spike_suffix, control_suffix, ('-5',))
sb.splits.assert_called_once_with(sample)
gc.genome_coverage.assert_any_call(sample, genome, scale, strand, input_suffix, output_suffix, spike_suffix, control_suffix, ('-5',))
gc.genome_coverage.assert_any_call(split1, genome, scale, strand, input_suffix, output_suffix, spike_suffix, control_suffix, ('-5',))
gc.genome_coverage.assert_any_call(split2, genome, scale, strand, input_suffix, output_suffix, spike_suffix, control_suffix, ('-5',))
def test_genome_coverage_scale_and_controlsuffix(testdir, mock_testclass):
sample = 'POLR2A'
bed = sample + '.bed'
cov = sample + '-cov.bed'
bw = sample + '-cov.bw'
genome = 'human.sizes'
control_suffix = '-input'
control = sample + control_suffix + '.bed'
count = 2000000
control_count = 300000
scale = BASE_SCALE / (count * control_count)
Bed.count_bed = MagicMock(side_effect=[count, control_count])
gc.coverage = MagicMock()
Bed.bedgraph_to_bigwig = MagicMock()
gc.genome_coverage(sample, genome, scale=1.5, control_suffix=control_suffix)
Bed.count_bed.assert_any_call(bed)
Bed.count_bed.assert_any_call(control)
gc.coverage.assert_called_once_with(bed, cov, genome, sample, scale, None, ())
Bed.bedgraph_to_bigwig.assert_called_once_with(cov, bw, genome)
def test_genome_coverage_scale_and_spikesuffix(testdir, mock_testclass):
sample = 'POLR2A'
bed = sample + '.bed'
cov = sample + '-cov.bed'
bw = sample + '-cov.bw'
genome = 'human.sizes'
spike_suffix = '-pombe'
spiked = sample + spike_suffix + '.bed'
count = 2000000
spiked_count = 400000
scale = BASE_SCALE * spiked_count / count
Bed.count_bed = MagicMock(side_effect=[count, spiked_count])
gc.coverage = MagicMock()
Bed.bedgraph_to_bigwig = MagicMock()
gc.genome_coverage(sample, genome, scale=1.5, spike_suffix=spike_suffix)
Bed.count_bed.assert_any_call(bed)
Bed.count_bed.assert_any_call(spiked)
gc.coverage.assert_called_once_with(bed, cov, genome, sample, scale, None, ())
Bed.bedgraph_to_bigwig.assert_called_once_with(cov, bw, genome)