def test_result_vec_to_features(self):
"Test lanthipeptides.result_vec_to_features()"
orig_feature = DummyCDS(0, 165)
orig_feature.locus_tag = 'FAKE0001'
seq = "TAILTAILTAILTAILTAILTAILTAILTAILTAILCC"
vec = Lanthipeptide(CleavageSiteHit(23, 42, 'Class-I'), 23,
"HEADHEADHEAD", seq)
motif = result_vec_to_feature(orig_feature, vec)
assert motif.location.start == 0
assert motif.location.end == 165
assert motif.location.strand == 1
assert motif.locus_tag == orig_feature.locus_tag
assert motif.score == 42
assert motif.detailed_information.rodeo_score == 23
assert motif.peptide_class == "lanthipeptide"
assert motif.peptide_subclass == "Class I"
assert motif.detailed_information.lan_bridges == 2
self.assertAlmostEqual(motif.molecular_weight, 3648.6, places=1)
self.assertAlmostEqual(motif.monoisotopic_mass, 3646.3, places=1)
for calc, expected in zip(
motif.alternative_weights,
[3666.6, 3684.6, 3702.7, 3720.7, 3738.7, 3756.7, 3774.7]):
self.assertAlmostEqual(calc, expected, places=1)
assert motif.core == seq
assert motif.leader == vec.leader
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
def setUp(self):
self.lant = Lanthipeptide(CleavageSiteHit(42, 17, 'Class-I'), 23, "HEAD", "MAGICHAT")