def test_peptide_plan_add(data, peptide_length, expected_len, expected_data):
plan = models.PeptidePlan(peptide_length)
for tup in data:
plan.add(tup)
assert (len(plan) == expected_len)
assert (plan.combinations == set(expected_data))
def peptide_plans(request):
plan_tup = request.getfixturevalue(request.param)
peptide_plan = models.PeptidePlan(plan_tup.length)
for tup in plan_tup.reg_combos + plan_tup.cap_combos:
peptide_plan.add(tup)
return peptide_plan
def generate(self, monomers, peptide_length, num_peptides):
c_cap_monomers = self._get_c_cap_monomers(monomers)
peptide_plan = models.PeptidePlan(peptide_length)
self._create_minimum_list(monomers, c_cap_monomers, peptide_plan)
self._create_remaining_list(monomers, c_cap_monomers, peptide_plan,
num_peptides)
return [peptide_plan]
def test_peptide_plan_iter(peptide_plan_data):
data, peptide_length = peptide_plan_data
plan = models.PeptidePlan(peptide_length)
for tup in data:
plan.add(tup)
for combination in plan:
assert (combination in data)
data.remove(combination)
def import_data(self, filepath, peptide_length):
peptide_plan = models.PeptidePlan(peptide_length)
num_lines_in_file = -1
for i, line in enumerate(utils.load_text(filepath)):
combo = tuple(map(int, line.strip('\n').split(',')))
peptide_plan.add(combo)
num_lines_in_file = i
self._validate_peptide_plan(peptide_plan, num_lines_in_file)
return self.saver.save([peptide_plan])
def test_peptide_plan_data(peptide_plan_data):
data, peptide_length = peptide_plan_data
plan = models.PeptidePlan(peptide_length)
for tup in data:
plan.add(tup)
plan_data = plan.data()
assert isinstance(plan_data, plan.PeptidePlanData)
assert isinstance(plan_data.reg_combos, np.ndarray)
assert isinstance(plan_data.cap_combos, np.ndarray)
assert np.array_equal(plan_data.reg_combos, np.array([data[0]]))
assert np.array_equal(plan_data.cap_combos, np.array([data[1]]))
assert plan_data.length == peptide_length
def test_peptide_plan_add_fail(data, peptide_length):
plan = models.PeptidePlan(peptide_length)
with pytest.raises(RuntimeError):
for tup in data:
plan.add(tup)
def test_peptide_plan_constructor(length):
plan = models.PeptidePlan(length)
assert plan.reg_length == length
assert plan.cap_length == length + 1