def create_descriptor():
"""Returns a ISA-Tab descriptor using a simple sample plan for
illustration."""
investigation = Investigation(identifier='I1')
plan = SampleAssayPlan()
plan.add_sample_type('liver')
plan.add_sample_plan_record('liver', 5)
plan.add_sample_type('blood')
plan.add_sample_plan_record('blood', 3)
plan.group_size = 2
f1 = StudyFactor(name='AGENT',
factor_type=OntologyAnnotation(term='pertubation agent'))
f2 = StudyFactor(name='INTENSITY',
factor_type=OntologyAnnotation(term='intensity'))
f3 = StudyFactor(name='DURATION',
factor_type=OntologyAnnotation(term='time'))
treatment_factory = TreatmentFactory(factors=[f1, f2, f3])
treatment_factory.add_factor_value(f1, {'cocaine', 'crack', 'aether'})
treatment_factory.add_factor_value(f2, {'low', 'medium', 'high'})
treatment_factory.add_factor_value(f3, {'short', 'long'})
ffactorial_design_treatments = treatment_factory\
.compute_full_factorial_design()
treatment_sequence = TreatmentSequence(
ranked_treatments=ffactorial_design_treatments)
# treatment_factory.add_factor_value('intensity', 1.05)
study = IsaModelObjectFactory(plan, treatment_sequence)\
.create_study_from_plan()
study.filename = 's_study.txt'
investigation.studies = [study]
print(isatab.dumps(investigation))
def test_create_study_from_plan(self):
plan = SampleAssayPlan()
plan.add_sample_type('liver')
plan.add_sample_plan_record('liver', 5)
plan.add_sample_type('blood')
plan.add_sample_plan_record('blood', 3)
plan.group_size = 2
treatment_factory = TreatmentFactory(
factors=[self.f1, self.f2, self.f3])
treatment_factory.add_factor_value(self.f1,
{'cocaine', 'crack', 'aether'})
treatment_factory.add_factor_value(self.f2, {'low', 'medium', 'high'})
treatment_factory.add_factor_value(self.f3, {'short', 'long'})
ffactorial_design_treatments = \
treatment_factory.compute_full_factorial_design()
treatment_sequence = TreatmentSequence(
ranked_treatments={(x, i)
for i, x in enumerate(
ffactorial_design_treatments)})
# makes each study group ranked in sequence
study = IsaModelObjectFactory(
plan, treatment_sequence).create_study_from_plan()
study.filename = 's_study.txt'
self.investigation.studies = [study]
self.assertEqual(36, len(study.sources))
self.assertEqual(288, len(study.samples))
def test_create_study_from_plan_with_qc(self):
plan = SampleAssayPlan()
plan.add_sample_type('liver')
plan.add_sample_plan_record('liver', 5)
plan.add_sample_type('blood')
plan.add_sample_plan_record('blood', 3)
plan.group_size = 2
plan.add_sample_type('solvent')
plan.add_sample_qc_plan_record('solvent', 8)
treatment_factory = TreatmentFactory(
factors=[self.f1, self.f2, self.f3])
treatment_factory.add_factor_value(self.f1,
{'cocaine', 'crack', 'aether'})
treatment_factory.add_factor_value(self.f2, {'low', 'medium', 'high'})
treatment_factory.add_factor_value(self.f3, {'short', 'long'})
ffactorial_design_treatments = \
treatment_factory.compute_full_factorial_design()
treatment_sequence = TreatmentSequence(
ranked_treatments={(x, i)
for i, x in enumerate(
ffactorial_design_treatments)})
# makes each study group ranked in sequence
study = IsaModelObjectFactory(
plan, treatment_sequence).create_study_from_plan()
study.filename = 's_study.txt'
# print(isatab.dumps(self.investigation))
self.investigation.studies = [study]
# 36 sources, 36 QC sources
self.assertEqual(72, len(study.sources))
self.assertEqual(
36,
len([
x for x in study.sources
if x.get_char('Material Type').value.term == 'solvent'
]))
# 288 samples plus 36 QC samples
self.assertEqual(324, len(study.samples))
def create_from_plan_parameters(galaxy_parameters_file,
sample_assay_plans_file, study_info_file,
treatment_plans_file, target_dir):
decoder = SampleAssayPlanDecoder()
if galaxy_parameters_file:
galaxy_parameters = json.load(galaxy_parameters_file)
sample_and_assay_plans, study_info, treatment_plan_params = \
map_galaxy_to_isa_create_json(galaxy_parameters)
plan = decoder.load(io.StringIO(json.dumps(sample_and_assay_plans)))
elif sample_assay_plans_file and study_info_file and treatment_plans_file:
plan = decoder.load(sample_assay_plans_file)
study_info = json.load(study_info_file)
treatment_plan_params = json.load(treatment_plans_file)
else:
raise IOError('Wrong parameters provided')
study_type = treatment_plan_params['study_type_cond']['study_type']
if study_type != 'intervention':
raise NotImplementedError('Only supports Intervention studies')
single_or_multiple = treatment_plan_params['study_type_cond'][
'one_or_more']['single_or_multiple']
if single_or_multiple == 'multiple':
raise NotImplementedError(
'Multiple treatments not yet implemented. Please select Single')
intervention_type = treatment_plan_params['study_type_cond'][
'one_or_more']['intervention_type']['select_intervention_type']
if intervention_type != 'chemical intervention':
raise NotImplementedError(
'Only Chemical Interventions supported at this time')
treatment_factory = TreatmentFactory(
intervention_type=INTERVENTIONS['CHEMICAL'], factors=BASE_FACTORS)
agent_levels = treatment_plan_params['study_type_cond']['one_or_more'][
'intervention_type']['agent'].split(',')
for agent_level in agent_levels:
treatment_factory.add_factor_value(BASE_FACTORS[0],
agent_level.strip())
dose_levels = treatment_plan_params['study_type_cond']['one_or_more'][
'intervention_type']['intensity'].split(',')
for dose_level in dose_levels:
treatment_factory.add_factor_value(BASE_FACTORS[1], dose_level.strip())
duration_of_exposure_levels = treatment_plan_params['study_type_cond'][
'one_or_more']['intervention_type']['duration'].split(',')
for duration_of_exposure_level in duration_of_exposure_levels:
treatment_factory.add_factor_value(BASE_FACTORS[2],
duration_of_exposure_level.strip())
treatment_sequence = TreatmentSequence(
ranked_treatments=treatment_factory.compute_full_factorial_design())
isa_object_factory = IsaModelObjectFactory(plan, treatment_sequence)
s = isa_object_factory.create_assays_from_plan()
contact = Person()
contact.affiliation = study_info['study_pi_affiliation']
contact.last_name = study_info['study_pi_last_name']
contact.email = study_info['study_pi_email']
contact.first_name = study_info['study_pi_first_name']
s.contacts = [contact]
s.description = study_info['study_description']
s.filename = 's_study.txt'
s.title = 'ISA created {}'.format(datetime.datetime.now().isoformat())
s.identifier = 'ISA-{}'.format(uuid.uuid4().hex[:8])
i = Investigation()
i.contacts = [contact]
i.description = s.description
i.title = s.title
i.identifier = s.identifier
i.studies = [s]
isatab.dump(isa_obj=i,
output_path=target_dir,
i_file_name='i_investigation.txt')
for assay in s.assays:
for data_file in assay.data_files:
data_file_path = os.path.join(target_dir, data_file.filename)
with open(data_file_path, 'a'):
os.utime(data_file_path, None)
class TreatmentFactoryTest(unittest.TestCase):
def setUp(self):
self.factory = TreatmentFactory()
def test_init(self):
self.assertEqual(self.factory.intervention_type,
INTERVENTIONS['CHEMICAL'])
self.assertTrue(isinstance(self.factory.factors, OrderedDict))
def test_add_factor_value_str(self):
factor = StudyFactor(name=BASE_FACTORS[0]['name'],
factor_type=BASE_FACTORS[0]['type'])
self.factory.add_factor_value(factor, 'agent_orange')
self.assertEqual(self.factory.factors.get(factor), {'agent_orange'})
def test_add_factor_value_number(self):
factor = StudyFactor(name=BASE_FACTORS[1]['name'],
factor_type=BASE_FACTORS[1]['type'])
self.factory.add_factor_value(factor, 1.05)
self.assertEqual(self.factory.factors.get(factor), {1.05})
def test_add_factor_value_list(self):
values_to_add = ['agent_orange', 'crack, cocaine']
factor = StudyFactor(name=BASE_FACTORS[0]['name'],
factor_type=BASE_FACTORS[0]['type'])
self.factory.add_factor_value(factor, values_to_add)
self.assertEqual(self.factory.factors.get(factor), set(values_to_add))
def test_add_factor_value_set(self):
values_to_add = {'agent_orange', 'crack, cocaine'}
factor = StudyFactor(name=BASE_FACTORS[0]['name'],
factor_type=BASE_FACTORS[0]['type'])
self.factory.add_factor_value(factor, values_to_add)
self.assertEqual(self.factory.factors.get(factor), values_to_add)
def test_compute_full_factorial_design(self):
agent = StudyFactor(name=BASE_FACTORS[0]['name'],
factor_type=BASE_FACTORS[0]['type'])
intensity = StudyFactor(name=BASE_FACTORS[1]['name'],
factor_type=BASE_FACTORS[1]['type'])
duration = StudyFactor(name=BASE_FACTORS[2]['name'],
factor_type=BASE_FACTORS[2]['type'])
self.factory.add_factor_value(agent, {'cocaine', 'crack', 'aether'})
self.factory.add_factor_value(intensity, {'low', 'medium', 'high'})
self.factory.add_factor_value(duration, {'short', 'long'})
full_factorial = self.factory.compute_full_factorial_design()
self.assertEqual(
full_factorial, {
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='cocaine'),
FactorValue(factor_name=intensity,
value='high'),
FactorValue(factor_name=duration,
value='long'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='cocaine'),
FactorValue(factor_name=intensity,
value='high'),
FactorValue(factor_name=duration,
value='short'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='cocaine'),
FactorValue(factor_name=intensity,
value='low'),
FactorValue(factor_name=duration,
value='long'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='cocaine'),
FactorValue(factor_name=intensity,
value='low'),
FactorValue(factor_name=duration,
value='short'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='cocaine'),
FactorValue(factor_name=intensity,
value='medium'),
FactorValue(factor_name=duration,
value='long'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='cocaine'),
FactorValue(factor_name=intensity,
value='medium'),
FactorValue(factor_name=duration,
value='short'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='crack'),
FactorValue(factor_name=intensity,
value='high'),
FactorValue(factor_name=duration,
value='long'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='crack'),
FactorValue(factor_name=intensity,
value='high'),
FactorValue(factor_name=duration,
value='short'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='crack'),
FactorValue(factor_name=intensity,
value='low'),
FactorValue(factor_name=duration,
value='long'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='crack'),
FactorValue(factor_name=intensity,
value='low'),
FactorValue(factor_name=duration,
value='short'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='crack'),
FactorValue(factor_name=intensity,
value='medium'),
FactorValue(factor_name=duration,
value='long'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='crack'),
FactorValue(factor_name=intensity,
value='medium'),
FactorValue(factor_name=duration,
value='short'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='aether'),
FactorValue(factor_name=intensity,
value='high'),
FactorValue(factor_name=duration,
value='long'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='aether'),
FactorValue(factor_name=intensity,
value='high'),
FactorValue(factor_name=duration,
value='short'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='aether'),
FactorValue(factor_name=intensity,
value='low'),
FactorValue(factor_name=duration,
value='long'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='aether'),
FactorValue(factor_name=intensity,
value='low'),
FactorValue(factor_name=duration,
value='short'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='aether'),
FactorValue(factor_name=intensity,
value='medium'),
FactorValue(factor_name=duration,
value='long'))),
Treatment(treatment_type=INTERVENTIONS['CHEMICAL'],
factor_values=(FactorValue(factor_name=agent,
value='aether'),
FactorValue(factor_name=intensity,
value='medium'),
FactorValue(factor_name=duration,
value='short')))
})
def test_compute_full_factorial_design_empty_agents(self):
agent = StudyFactor(name=BASE_FACTORS[0]['name'],
factor_type=BASE_FACTORS[0]['type'])
intensity = StudyFactor(name=BASE_FACTORS[1]['name'],
factor_type=BASE_FACTORS[1]['type'])
duration = StudyFactor(name=BASE_FACTORS[2]['name'],
factor_type=BASE_FACTORS[2]['type'])
self.factory.add_factor_value(agent, set())
self.factory.add_factor_value(intensity, {'low', 'medium', 'high'})
self.factory.add_factor_value(duration, {'short', 'long'})
full_factorial = self.factory.compute_full_factorial_design()
self.assertEqual(full_factorial, set())
def test_compute_full_factorial_design_empty_intensities(self):
agent = StudyFactor(name=BASE_FACTORS[0]['name'],
factor_type=BASE_FACTORS[0]['type'])
intensity = StudyFactor(name=BASE_FACTORS[1]['name'],
factor_type=BASE_FACTORS[1]['type'])
duration = StudyFactor(name=BASE_FACTORS[2]['name'],
factor_type=BASE_FACTORS[2]['type'])
self.factory.add_factor_value(agent, {'cocaine', 'crack', 'aether'})
self.factory.add_factor_value(intensity, set())
self.factory.add_factor_value(duration, {'short', 'long'})
full_factorial = self.factory.compute_full_factorial_design()
self.assertEqual(full_factorial, set())