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_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_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_multiplex_three_guides(temp_dir, data_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 = "UUCCCCUUAUUUAGAUAACU,UCCCCUUAUUUAGAUAACUC,UGUUAACCAAAUUAUGAUGA"
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'] == 63
assert len(results['guides']) == 3
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)
def test_donor_substitution_example(temp_dir, data_dir):
""" Running a good sample with donor containing only a 2bp substitution """
control = os.path.join(data_dir, 'donor_sub_example_control.ab1')
sample = os.path.join(data_dir, 'donor_sub_example_edited.ab1')
output_path = os.path.join(temp_dir, 'donor_example')
# this should result in a 2bp substitution
guide = 'GCTGCTTCCTGGGGGCGCCT'
donor = 'AGCCTCAGGGCCTCACACCAGCCCATGTGGATGACCTGAGGGTCCTGTTTCCCATCCCACttCAGGCGCCCCCAGGAAGCAGCGGCGGGAGCGCACCACCTTCACCCGGAGCCAACTGGAGG'
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 pytest.approx(results['hdr_pct']) == 44
def test_lowercase_guide(temp_dir, data_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_lowercase')
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'] == 77
allproposals = os.path.join(temp_dir,
'high_quality_lowercase.allproposals.json')
assert os.path.exists(allproposals)
def test_multiplex_three_guides_no_editing(temp_dir, data_dir):
"""
Running a zero editing multiplex sample, with guides that are far apart
"""
control = os.path.join(data_dir, "multiplex1_control.ab1")
sample = os.path.join(data_dir, "multiplex1_control.ab1")
output_path = os.path.join(temp_dir, 'multiplex_no_editing_far_guides')
guide = "UUCCCCUUAUUUAGAUAACU,UCCCCUUAUUUAGAUAACUC,TGAGTTTTTTTGTAAGTAGC"
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'] == 0
assert len(results['guides']) == 3
from pprint import pprint as pp
from ice.analysis import single_sanger_analysis, multiple_sanger_analysis
# Running a single analysis
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,
