def test_ignore_strand_sample_split(testdir, mock_testclass): split = 'POLR2A-100-110' bed = split + '.bed' forcov = split + '-forcov.bed' igs.ignore_strand = MagicMock() igs.ignore_strand_sample(split) igs.ignore_strand.assert_called_once_with(bed, forcov)
def test_ignore_strand_sample(testdir, mock_testclass): sample = 'POLR2A' bed = sample + '.bed' forcov = sample + '-forcov.bed' igs.ignore_strand = MagicMock() igs.ignore_strand_sample(sample) igs.ignore_strand.assert_called_once_with(bed, forcov)
def test_ignore_strand_sample_splits_notsplits(testdir, mock_testclass): sample = 'POLR2A' splits = [] igs.ignore_strand_sample = MagicMock() sb.splits = MagicMock(return_value=splits) igs.ignore_strand_sample_splits(sample) igs.ignore_strand_sample.assert_called_once_with(sample, '', '-forcov')
def test_ignore_strand_samples(testdir, mock_testclass): samples_file = Path(__file__).parent.joinpath('samples.txt') samples = ['POLR2A', 'ASDURF', 'POLR1C'] Parser.first = MagicMock(return_value=samples) igs.ignore_strand_sample_splits = MagicMock() igs.ignore_strand_samples(samples_file) Parser.first.assert_called_once_with(samples_file) for sample in samples: igs.ignore_strand_sample_splits.assert_any_call(sample, '', '-forcov')
def test_ignore_strand_sample_parameters(testdir, mock_testclass): sample = 'POLR2A' input_suffix = '-input' output_suffix = '-output' bed = sample + input_suffix + '.bed' forcov = sample + output_suffix + '.bed' igs.ignore_strand = MagicMock() igs.ignore_strand_sample(sample, input_suffix, output_suffix) igs.ignore_strand.assert_called_once_with(bed, forcov)
def test_ignore_strand_sample_splits(testdir, mock_testclass): sample = 'POLR2A' splits = ['POLR2A-100-110', 'POLR2A-120-130'] igs.ignore_strand_sample = MagicMock() sb.splits = MagicMock(return_value=splits) igs.ignore_strand_sample_splits(sample) igs.ignore_strand_sample.assert_any_call(sample, '', '-forcov') for split in splits: igs.ignore_strand_sample.assert_any_call(split, '', '-forcov')
def test_ignore_strand_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) igs.ignore_strand_sample_splits = MagicMock() igs.ignore_strand_samples(samples_file, input_suffix, output_suffix) Parser.first.assert_called_once_with(samples_file) for sample in samples: igs.ignore_strand_sample_splits.assert_any_call( sample, input_suffix, output_suffix)
def test_ignore_strand_sample_splits_parameters(testdir, mock_testclass): sample = 'POLR2A' input_suffix = '-input' output_suffix = '-output' splits = ['POLR2A-100-110', 'POLR2A-120-130'] igs.ignore_strand_sample = MagicMock() sb.splits = MagicMock(return_value=splits) igs.ignore_strand_sample_splits(sample, input_suffix, output_suffix) igs.ignore_strand_sample.assert_any_call(sample, input_suffix, output_suffix) for split in splits: igs.ignore_strand_sample.assert_any_call(split, input_suffix, output_suffix)
def test_ignore_strand(testdir, mock_testclass): bed = Path(__file__).parent.joinpath('sample.bed') forcov = 'POLR2A-forcov.bed' igs.ignore_strand(bed, forcov) with open(forcov, 'r') as infile: infile.readline() == 'chr1\t100\t150\ttest1\t1\t+\n' infile.readline() == 'chr1\t100\t150\ttest1\t1\t-\n' infile.readline() == 'chr2\t400\t450\ttest2\t2\t+\n' infile.readline() == 'chr2\t400\t450\ttest2\t2\t-\n' infile.readline() == 'chr3\t500\t650\ttest3\t3\t+\n' infile.readline() == 'chr3\t500\t650\ttest3\t3\t-\n' infile.readline() == 'chr4\t800\t750\ttest4\t4\t+\n' infile.readline() == 'chr4\t800\t750\ttest4\t4\t-\n' infile.readline() == 'chr5\t100\t150\ttest5\t1\t-\n' infile.readline() == 'chr5\t100\t150\ttest5\t1\t+\n' infile.readline() == 'chr6\t400\t450\ttest6\t2\t-\n' infile.readline() == 'chr6\t400\t450\ttest6\t2\t+\n' infile.readline() == 'chr7\t500\t650\ttest7\t3\t-\n' infile.readline() == 'chr7\t500\t650\ttest7\t3\t+\n' infile.readline() == 'chr8\t800\t750\ttest8\t4\t-\n' infile.readline() == 'chr8\t800\t750\ttest8\t4\t+\n'