def test_at_spec(self, mocked_get, mocked_match):
mocked_match.return_value = True
for sig in ["HF", "YS", "HS", "YF", "NN"]:
mocked_get.return_value = [
DummyAlignment(sig, {
195: sig[0],
197: sig[1]
})
]
pairings = analysis.pksi_at_spec(self.record)
if sig == "HF":
assert pairings == [(sig, "Malonyl-CoA specific")]
elif sig == "YS":
assert pairings == [(sig, "Methylmalonyl-CoA specific")]
else:
assert pairings == [
(sig, "Neither malonyl-CoA or methylmalonyl-CoA specific")
]
# and an inconclusive
mocked_match.return_value = False
# values here don't matter
mocked_get.return_value = [DummyAlignment("incon", {})]
pairings = analysis.pksi_at_spec(self.record)
assert pairings == [("incon",
"(Methyl)Malonyl-CoA specificity inconclusive")]
def test_at_spec(self):
with umock.patch.object(active_site_finder.common.ActiveSiteAnalysis,
"scaffold_matches") as mocked_match:
mocked_match.return_value = True
for sig in ["HF", "YS", "HS", "YF", "NN"]:
mock(
"active_site_finder.common.ActiveSiteAnalysis.get_alignments",
returns=[DummyAlignment(sig, {
195: sig[0],
197: sig[1]
})])
pairings = analysis.pksi_at_spec(self.record)
if sig == "HF":
assert pairings == [(sig, "Malonyl-CoA specific")]
elif sig == "YS":
assert pairings == [(sig, "Methylmalonyl-CoA specific")]
else:
assert pairings == [
(sig,
"Neither malonyl-CoA or methylmalonyl-CoA specific")
]
# and an inconclusive
mocked_match.return_value = False
# values here don't matter
mock("active_site_finder.common.ActiveSiteAnalysis.get_alignments",
returns=[DummyAlignment("incon", {})])
pairings = analysis.pksi_at_spec(self.record)
assert pairings == [
("incon", "(Methyl)Malonyl-CoA specificity inconclusive")
]
def test_AT_spec(self):
mock("subprocessing.run_hmmpfam2", returns=parse_hmmpfam_results("AT.output"))
results = analysis.pksi_at_spec(self.record)
expected = {'PKS_AT0': '(Methyl)Malonyl-CoA specificity inconclusive',
'PKS_AT1': 'Neither malonyl-CoA or methylmalonyl-CoA specific',
'PKS_AT2': '(Methyl)Malonyl-CoA specificity inconclusive',
'PKS_AT3': '(Methyl)Malonyl-CoA specificity inconclusive'}
assert {dom.domain_id: message for dom, message in results} == expected