def test_center_annotations_sample(testdir, mock_testclass): sample = 'POLR2A' bed = sample + '.bed' forcov = sample + '-forcov.bed' ca.center_annotations = MagicMock() ca.center_annotations_sample(sample) ca.center_annotations.assert_called_once_with(bed, forcov)
def test_center_annotations_sample_split(testdir, mock_testclass): split = 'POLR2A-100-110' bed = split + '.bed' forcov = split + '-forcov.bed' ca.center_annotations = MagicMock() ca.center_annotations_sample(split) ca.center_annotations.assert_called_once_with(bed, forcov)
def test_center_annotations_sample_splits_notsplits(testdir, mock_testclass): sample = 'POLR2A' splits = [] ca.center_annotations_sample = MagicMock() sb.splits = MagicMock(return_value=splits) ca.center_annotations_sample_splits(sample) ca.center_annotations_sample.assert_called_once_with(sample, '', '-forcov')
def test_center_annotations_sample_parameters(testdir, mock_testclass): sample = 'POLR2A' input_suffix = '-input' output_suffix = '-output' bed = sample + input_suffix + '.bed' forcov = sample + output_suffix + '.bed' ca.center_annotations = MagicMock() ca.center_annotations_sample(sample, input_suffix, output_suffix) ca.center_annotations.assert_called_once_with(bed, forcov)
def test_center_annotations_sample_splits(testdir, mock_testclass): sample = 'POLR2A' splits = ['POLR2A-100-110', 'POLR2A-120-130'] ca.center_annotations_sample = MagicMock() sb.splits = MagicMock(return_value=splits) ca.center_annotations_sample_splits(sample) ca.center_annotations_sample.assert_any_call(sample, '', '-forcov') for split in splits: ca.center_annotations_sample.assert_any_call(split, '', '-forcov')
def test_center_annotations_samples_second(testdir, mock_testclass): samples_file = Path(__file__).parent.joinpath('samples.txt') samples = ['POLR2A', 'ASDURF', 'POLR1C'] Parser.first = MagicMock(return_value=samples) ca.center_annotations_sample_splits = MagicMock() ca.center_annotations_samples(samples_file, index=1) Parser.first.assert_called_once_with(samples_file) ca.center_annotations_sample_splits.assert_called_once_with( samples[1], '', '-forcov')
def test_center_annotations_samples_parameters(testdir, mock_testclass): samples_file = Path(__file__).parent.joinpath('samples.txt') input_suffix = '-input' output_suffix = '-output' samples = ['POLR2A', 'ASDURF', 'POLR1C'] Parser.first = MagicMock(return_value=samples) ca.center_annotations_sample_splits = MagicMock() ca.center_annotations_samples(samples_file, input_suffix, output_suffix) Parser.first.assert_called_once_with(samples_file) for sample in samples: ca.center_annotations_sample_splits.assert_any_call( sample, input_suffix, output_suffix)
def test_center_annotations(testdir, mock_testclass): bed = Path(__file__).parent.joinpath('sample.bed') forcov = 'POLR2A-forcov.bed' ca.center_annotations(bed, forcov) with open(forcov, 'r') as infile: infile.readline() == 'chr1\t125\t126\ttest1\t1\t+\n' infile.readline() == 'chr2\t425\t426\ttest2\t2\t+\n' infile.readline() == 'chr3\t575\t576\ttest3\t3\t+\n' infile.readline() == 'chr4\t775\t775\ttest4\t4\t+\n' infile.readline() == 'chr5\t125\t126\ttest5\t1\t-\n' infile.readline() == 'chr6\t425\t426\ttest6\t2\t-\n' infile.readline() == 'chr7\t575\t576\ttest7\t3\t-\n' infile.readline() == 'chr8\t875\t776\ttest8\t4\t-\n'
def test_center_annotations_sample_splits_parameters(testdir, mock_testclass): sample = 'POLR2A' input_suffix = '-input' output_suffix = '-output' splits = ['POLR2A-100-110', 'POLR2A-120-130'] ca.center_annotations_sample = MagicMock() sb.splits = MagicMock(return_value=splits) ca.center_annotations_sample_splits(sample, input_suffix, output_suffix) ca.center_annotations_sample.assert_any_call(sample, input_suffix, output_suffix) for split in splits: ca.center_annotations_sample.assert_any_call(split, input_suffix, output_suffix)