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'