def test_reconstruction(self):
preds_by_cds = build_dummy_cds_predictions()
starters = [Prediction('acetyl', 0., 0.)]
elongations = [Prediction('7', 743.5, 1.2e-226)]
classes = {"benzoisochromanequinone"}
weights = {"acetyl_7": 451.23}
cluster_pred = ProtoclusterPrediction(preds_by_cds,
starter_units=starters,
malonyl_elongations=elongations,
product_classes=classes,
molecular_weights=weights,
start=100,
end=2000)
assert cluster_pred.cds_predictions == preds_by_cds
assert cluster_pred.starter_units == starters
assert cluster_pred.malonyl_elongations == elongations
assert cluster_pred.product_classes == classes
assert cluster_pred.molecular_weights == weights
assert cluster_pred.start == 100
assert cluster_pred.end == 2000
reconstructed = ProtoclusterPrediction.from_json(
json.loads(json.dumps(cluster_pred.to_json())))
assert cluster_pred.cds_predictions == preds_by_cds
assert reconstructed.starter_units == starters
assert reconstructed.malonyl_elongations == elongations
assert reconstructed.product_classes == classes
assert reconstructed.molecular_weights == weights
assert reconstructed.start == 100
assert reconstructed.end == 2000
def test_invalid(self):
with self.assertRaisesRegex(ValueError,
"could not convert string to float"):
Prediction("name", "not a float", 1e-89)
with self.assertRaisesRegex(ValueError,
"could not convert string to float"):
Prediction("name", 1e-89, "not a float")
def build_dummy_cluster_prediction():
return ClusterPrediction(build_dummy_cds_predictions(),
[Prediction('acetyl', 0., 0.)],
[Prediction('7', 743.5, 1.2e-226)],
{"benzoisochromanequinone"}, {"acetyl_7": 451.23},
start=0,
end=1500)
def test_coelicolor_c11(self, _mocked_blastp):
with patch.object(t2pks_analysis, "run_t2pks_hmmscan", return_value=self.hmm_results()):
results = t2pks_analysis.analyse_cluster(self.cluster, self.record)
assert isinstance(results, ProtoclusterPrediction)
assert results.product_classes == {"benzoisochromanequinone"}
assert results.starter_units == [Prediction("acetyl-CoA", 0., 0.)]
assert results.malonyl_elongations == [Prediction("7", 743.5, 1.2e-226)]
assert list(results.molecular_weights) == ["acetyl-CoA_7"]
self.assertAlmostEqual(results.molecular_weights["acetyl-CoA_7"], 342.3845)
def test_coelicolor_c11(self):
results = t2pks_analysis.analyse_cluster(self.cluster, self.record)
assert isinstance(results, ClusterPrediction)
assert results.product_classes == {"benzoisochromanequinone"}
assert results.starter_units == [Prediction("acetyl-CoA", 0., 0.)]
assert results.malonyl_elongations == [
Prediction("7", 743.5, 1.2e-226)
]
assert list(results.molecular_weights) == ["acetyl-CoA_7"]
self.assertAlmostEqual(results.molecular_weights["acetyl-CoA_7"],
342.3845)
def test_equality(self):
first = Prediction("somename", 15., 1e-89)
second = Prediction("somename", 15., 1e-89)
assert first == second
second = Prediction("tomename", 15., 1e-89)
assert first != second
second = Prediction("somename", 1., 1e-89)
assert first != second
second = Prediction("tomename", 15., 1e-88)
assert first != second
assert first != "not a Prediction"
def test_reconstruction(self):
pred = Prediction("somename", 15., 1e-89)
reconstructed = Prediction.from_json(
json.loads(json.dumps(pred.to_json())))
assert pred is not reconstructed
assert pred == reconstructed
def test_stringification(self):
pred = Prediction("somename", 15., 1e-89)
assert str(pred) == "somename (Score: 15.0; E-value: 1e-89)"