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)