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
def test_low_quality_control(temp_dir):
#Low quality control but analysis still possible
control = os.path.join(data_dir(), "low_quality_control2.ab1")
sample = os.path.join(data_dir(), "low_quality_edited2.ab1")
guide = 'CUGGUCGCGCACGAUCAGGG'
output_path = os.path.join(temp_dir, 'low_quality')
job_args = (control, sample, output_path, guide)
job_kwargs = {'verbose': True}
results = single_sanger_analysis(*job_args, **job_kwargs)
assert 'Low quality control trace' in results['notes']
def test_low_quality_control_fail(temp_dir):
#Low quality control trace --> no analysis possible
bad_quality = os.path.join(data_dir(), "low_quality_control.ab1")
sample = os.path.join(data_dir(), "good_example_edited.ab1")
guide = 'CCCGCCTCGGCCTCCCTAA'
output_path = os.path.join(temp_dir, 'low_quality')
job_args = (bad_quality, sample, output_path, guide)
job_kwargs = {'verbose': True}
results = single_sanger_analysis(*job_args, **job_kwargs)
assert results['status'] == 'succeeded'
assert 'Control ab1 trace quality scores too low' in results['notes']
def test_sanger_analysis_bad_path(temp_dir):
sa = SangerAnalysis()
bad_file = os.path.join(data_dir(), "no_file_here.xyz")
control = os.path.join(data_dir(), "good_example_control.ab1")
sample = os.path.join(data_dir(), "good_example_edited.ab1")
guide = "CGGCUCAAAAGGACCAGACU"
with pytest.raises(Exception):
sa.initialize_with(bad_file, sample, guide)
with pytest.raises(Exception):
sa.initialize_with(control, bad_file, guide)
with pytest.raises(Exception):
sa.initialize_with(control, sample, 123)
with pytest.raises(Exception):
sa.initialize_with(control, sample, "1234")
def test_bad_paths(temp_dir):
control = os.path.join(data_dir(), "does_not_exist.abcxyz")
sample = os.path.join(data_dir(), "alignment_fail_edited.ab1")
output_path = os.path.join(temp_dir, 'bad_paths')
guide = "AACCAGTTGCAGGCGCCCCA"
job_args = (control, sample, output_path, guide)
job_kwargs = {'verbose': True}
with pytest.raises(Exception):
results = single_sanger_analysis(*job_args, **job_kwargs)
good_control = os.path.join(data_dir(), "low_quality_control.ab1")
bad_sample = os.path.join(data_dir(), "does_not_exist.abcxyz")
job_args = (good_control, bad_sample, output_path, guide)
job_kwargs = {'verbose': True}
with pytest.raises(Exception):
results = single_sanger_analysis(*job_args, **job_kwargs)
def test_multiplex_1_1(temp_dir):
""" Running a good multiplex sample"""
control = os.path.join(data_dir(), "multiplex1_control.ab1")
sample = os.path.join(data_dir(), "multiplex1_edited.ab1")
output_path = os.path.join(temp_dir, 'multiplex1')
guide = "UCCCCUUAUUUAGAUAACUC"
job_args = (control, sample, output_path, guide)
job_kwargs = {'verbose': True}
results = single_sanger_analysis(*job_args, **job_kwargs)
pp(results)
assert results['status'] == 'succeeded'
assert results['ice_d'] == 67
def test_donor_example(temp_dir):
"""Running a good sample with HDR"""
control = os.path.join(data_dir(), "donor_example_control.ab1")
sample = os.path.join(data_dir(), "donor_example_knockin.ab1")
output_path = os.path.join(temp_dir, 'donor_example')
guide = "AAGTGCAGCTCGTCCGGCGT"
donor = 'ATCCTCCCGGGAACGTCTCCACCAGCTTCCCTTCCAGCCGACGAGATTGATCTCCGACCCGACGAGCTGCACTTCCTGTCCAAGCACTTCCGCAGCTCAGAGAA'
job_args = (control, sample, output_path, guide, donor)
job_kwargs = {'verbose': True}
results = single_sanger_analysis(*job_args, **job_kwargs)
pp(results)
assert results['status'] == 'succeeded'
assert results['hdr_pct'] > 20
def test_sequence_not_found(temp_dir):
control = os.path.join(data_dir(), "bad_guide_sequence_control.ab1")
sample = os.path.join(data_dir(), "bad_guide_sequence_edited.ab1")
output_path = os.path.join(temp_dir, 'bad_sequence')
guide = "AACCAGTTGCAGGCGCCCCA"
job_args = (control, sample, output_path, guide)
job_kwargs = {'verbose': True}
try:
results = single_sanger_analysis(*job_args, **job_kwargs)
assert False
except Exception as e:
pp(results)
assert results['status'] == 'succeeded'
assert 'guide AACCAGTTGCAGGCGCCCCA not found in control sequence' in results[
'notes']
def test_alignment_fail(temp_dir):
control = os.path.join(data_dir(), "alignment_fail_control.ab1")
sample = os.path.join(data_dir(), "alignment_fail_edited.ab1")
output_path = os.path.join(temp_dir, 'alignment_fail')
guide = "AACCAGTTGCAGGCGCCCCA"
job_args = (control, sample, output_path, guide)
job_kwargs = {'verbose': True}
try:
results = single_sanger_analysis(*job_args, **job_kwargs)
assert False
except Exception as e:
pp(results)
assert results['status'] == 'succeeded'
assert "No alignment found between control and edited sample" in results[
'notes']
def test_low_quality_sample(temp_dir):
""" Running a low quality sample"""
control = os.path.join(data_dir(), "low_quality_control.ab1")
sample = os.path.join(data_dir(), "low_quality_edited.ab1")
output_path = os.path.join(temp_dir, 'low_quality')
guide = "CGGCUCAAAAGGACCAGACU"
# guide = 'AAAGUCAUCCAAGCCAAGUC'
# guide = 'CAAAAGGACCAGACUUGGCU'
job_args = (control, sample, output_path, guide)
job_kwargs = {'verbose': True}
#low quality sample
results = single_sanger_analysis(*job_args, **job_kwargs)
assert results['status'] == 'succeeded'
assert 'Sample ab1 low_quality_edited.ab1 quality scores too low' in results[
'notes']
def test_high_quality_sample(temp_dir):
""" Running a good sample"""
control = os.path.join(data_dir(), "good_example_control.ab1")
sample = os.path.join(data_dir(), "good_example_edited.ab1")
output_path = os.path.join(temp_dir, 'high_quality')
guide = "AACCAGTTGCAGGCGCCCCA"
job_args = (control, sample, output_path, guide)
job_kwargs = {'verbose': True, 'allprops': True}
results = single_sanger_analysis(*job_args, **job_kwargs)
pp(results)
assert results['status'] == 'succeeded'
assert results['ice'] == 78
allproposals = os.path.join(temp_dir, 'high_quality.allproposals.json')
assert os.path.exists(allproposals)
