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import pytest
from bcbio.rnaseq import ericscript
from tests.unit.conftest import DummyFileTransaction
@pytest.fixture
def utils(mocker):
yield mocker.patch('bcbio.rnaseq.ericscript.utils')
class TestGetInputData(object):
def test_get_disambiguated_bam(self, mocker):
sample_config = {
'config': {
'algorithm': {
'disambiguate': ['mm9'],
}
},
'work_bam':
'/path/to/disambiguate_star/Test1.nsorted.human.sorted.bam',
'dirs': {'work': '/path/to/workdir'},
}
convert = mocker.patch('bcbio.rnaseq.ericscript.convert_bam_to_fastq')
result = ericscript.prepare_input_data(sample_config)
convert.assert_called_once_with(
sample_config['work_bam'],
sample_config['dirs']['work'],
None, None, sample_config
)
assert result == convert.return_value
def test_get_fastq_input_files_if_no_disambiguation(self):
fq_files = (
'/path/to/1_1_trimmed.fq.gz',
'/path/to/1_2_trimmed.fq.gz'
)
sample_config = {'files': list(fq_files)}
result = ericscript.prepare_input_data(sample_config)
assert result == fq_files
class TestRun(object):
@pytest.fixture
def mock_ft(self, mocker):
yield mocker.patch(
'bcbio.rnaseq.ericscript.file_transaction',
side_effect=DummyFileTransaction
)
@pytest.fixture
def do_run(self, mocker):
yield mocker.patch(
'bcbio.rnaseq.ericscript.do.run',
autospec=True
)
@pytest.fixture
def prepare_data(self, mocker):
yield mocker.patch('bcbio.rnaseq.ericscript.prepare_input_data')
|
