def test_module_for_orphans(self):
for name in [
NRPS_START, NRPS_LOAD, PKS_START, PKS_LOAD, "cMT", "ACP",
"Trans-AT_docking"
]:
modules = build_modules_for_cds([DummyHMMResult(name)],
[DummyHMMResult("")])
assert len(modules) == 1
assert not modules[0].is_complete()
def test_starters(self):
for domain_type in [NRPS_LOAD, PKS_LOAD]:
domains = [DummyHMMResult(i) for i in [domain_type, "ACP", domain_type, "ACP"]]
modules = build_modules_for_cds(domains, [])
print(modules)
assert len(modules) == 2
assert modules[0]._first_in_cds
assert modules[0].is_complete()
assert not modules[1]._first_in_cds
print(modules[1], modules[1].is_complete())
print(modules[1]._starter, modules[1]._loader, modules[1]._carrier_protein, modules[1]._starter is modules[1]._loader)
assert not modules[1].is_complete()
def test_bad_add_makes_new_module(self):
modules = build_modules_for_cds([DummyHMMResult(NRPS_LOAD)] * 2, [])
assert len(modules) == 2
assert not modules[0].is_complete()
def test_module_for_each_starter(self):
modules = build_modules_for_cds([
DummyHMMResult("Condensation_DCL"),
DummyHMMResult("Condensation_LCL")
], [])
assert len(modules) == 2
def test_unclassifiable(self):
with self.assertRaisesRegex(ValueError, "could not classify domain"):
build_modules_for_cds([DummyHMMResult("UNCLASSIFIABLE")], [])
def test_no_empties(self):
assert build_modules_for_cds([], []) == []
assert build_modules_for_cds([DummyHMMResult("ACPS")], []) == []
def test_mismatching_ks_subtypes(self):
with self.assertRaises(StopIteration):
build_modules_for_cds([DummyHMMResult(PKS_START)], [])