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_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_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)