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_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_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',))