def test_prediction_with_core_class2(self, _patched_rodeo):
# the cleavage result adjusted to leave at least one amino in core
cleavage_result = CleavageSiteHit(end=40, score=-6.8, lantype="Class-II")
with patch.object(lanthi, "predict_cleavage_site", return_value=cleavage_result):
results = run_lanthipred(DummyRecord(features=[self.cds]),
self.cds, "Class-II", self.domains)
assert results is not None
assert str(results).startswith("Lanthipeptide(..40, -6.8, 'Class-II', 'LSQGLGGC', 1, 715")
def test_prediction_with_no_core(self):
# the real cleavage site result (+1 at end for the C)
cleavage_result = CleavageSiteHit(end=48,
score=-6.8,
lantype="Class-II")
mock("lanthi.predict_cleavage_site", returns=cleavage_result)
for part in ["I", "II"]:
assert run_lanthipred(None, self.cds, "Class-%s" % part,
self.domains) is None
def test_prediction_with_core_class1(self):
# the cleavage result adjusted to leave at least one amino in core
cleavage_result = CleavageSiteHit(end=40,
score=-6.8,
lantype="Class-I")
mock("lanthi.predict_cleavage_site", returns=cleavage_result)
results = run_lanthipred(DummyRecord(features=[self.cds]), self.cds,
"Class-I", self.domains)
assert results
assert str(results).startswith(
"Lanthipeptide(..40, -6.8, 'Class-I', 'LSQGLGGC', 1, 715")
def test_prediction_with_no_core(self, _patched_rodeo):
# the real cleavage site result (+1 at end for the C)
cleavage_result = CleavageSiteHit(end=48,
score=-6.8,
lantype="Class-II")
with patch.object(lanthi,
"predict_cleavage_site",
return_value=cleavage_result):
for part in ["I", "II"]:
assert run_lanthipred(None, self.cds, "Class-%s" % part,
self.domains) is None
def test_prediction_with_core(self):
# the cleavage result adjusted to leave at least one amino in core
cleavage_result = CleavageSiteHit(start=38,
end=40,
score=-6.8,
lantype="Class-II")
mock("lanthi.predict_cleavage_site", returns=cleavage_result)
for part in ["I", "II"]:
results = run_lanthipred(DummyRecord(features=[self.cds]),
self.cds, "Class-%s" % part, self.domains)
assert results is not None