def test_batch_analysis(temp_dir):
""" Execute a batch analysis"""
definition_file = os.path.join(data_dir(), 'batch_example.xlsx')
data_directory = data_dir()
output_dir = os.path.join(temp_dir, 'batch_analysis')
job_args = (definition_file, output_dir)
job_kwargs = {'verbose': True, 'data_dir': data_directory}
results = multiple_sanger_analysis(*job_args, **job_kwargs)
pp(results)
for idx, result in enumerate(results):
if idx == 1:
assert result['sample_name'] == 'multiplex_example1'
guides = []
expected_guides = [
'UGCCAGGAUCACCUCCGAGA'.replace('U', 'T'),
'CGAUAGGGGGGCCUUCUCGG'.replace('U', 'T'),
'GCGUCCUCUUAUCUUCUGCC'.replace('U', 'T')
]
for g in result['guides']:
guides.append(g['sequence'])
assert set(expected_guides) == set(guides)
if idx == 6:
assert result['sample_name'] == 'test_revcomp'
assert result['guides'][0]['sequence'] == 'CCAGAGGCTGATGCTCACCA'
if idx == 8:
msg = "Could not analyze homologous recombination case: "
msg += "Homology arms of length {} not found in control sequence".format(
EditProposalCreator.MIN_HOMOLOGY_ARM)
assert result['notes'] == msg
def test_bad_batch(temp_dir):
definition_file = os.path.join(data_dir(), 'bad_batch_definition.xlsx')
data_directory = data_dir()
output_dir = os.path.join(temp_dir, 'bad_batch_analysis')
job_args = (definition_file, output_dir)
job_kwargs = {'verbose': True, 'data_dir': data_directory}
results = multiple_sanger_analysis(*job_args, **job_kwargs)
assert not results
control_path = os.path.abspath('./ice/tests/test_data/good_example_control.ab1')
sample_path = os.path.abspath('./ice/tests/test_data/good_example_edited.ab1')
guide = 'AACCAGTTGCAGGCGCCCCA'
base_outputname = './results/good_example'
donor = None
verbose = True
results = single_sanger_analysis(control_path=control_path,
sample_path=sample_path,
base_outputname=base_outputname,
guide=guide,
donor=donor,
verbose=verbose)
pp(results)
# Running a batch analysis
definition_file = os.path.abspath('./ice/tests/test_data/batch_example.xlsx')
data_directory = os.path.abspath('./ice/tests/test_data/')
output_dir = './results/batch_example'
job_args = (definition_file, output_dir)
job_kwargs = {
'verbose': True,
'data_dir': data_directory
}
multiple_sanger_analysis(*job_args, **job_kwargs)