def test_er_stereo(self):
with umock.patch.object(active_site_finder.common.ActiveSiteAnalysis,
"scaffold_matches") as mocked_match:
mocked_match.return_value = True
for char in string.ascii_uppercase:
mock(
"active_site_finder.common.ActiveSiteAnalysis.get_alignments",
returns=[DummyAlignment(char, {39: char})])
pairings = analysis.pksi_er_stereo(self.record)
if char == "Y":
assert pairings == [(
char,
"ER domain putatively catalyzing 2S-configuration product formation"
)]
else:
assert pairings == [(
char,
"ER domain putatively catalyzing 2R-configuration product formation"
)]
# 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_er_stereo(self.record)
assert pairings == [("incon", "ER configuration inconclusive")]
def test_er_stereo(self, mocked_get, mocked_match):
mocked_match.return_value = True
for char in string.ascii_uppercase:
mocked_get.return_value = [DummyAlignment(char, {39: char})]
pairings = analysis.pksi_er_stereo(self.record)
if char == "Y":
assert pairings == [(char, "ER domain putatively catalyzing 2S-configuration product formation")]
else:
assert pairings == [(char, "ER domain putatively catalyzing 2R-configuration product formation")]
# and an inconclusive
mocked_match.return_value = False
# values here don't matter
mocked_get.return_value = [DummyAlignment("incon", {})]
pairings = analysis.pksi_er_stereo(self.record)
assert pairings == [("incon", "ER configuration inconclusive")]
def test_ER(self):
mock("subprocessing.run_hmmpfam2", returns=parse_hmmpfam_results("ER.output"))
results = analysis.pksi_er_stereo(self.record)
expected = {'Thioesterase0': 'active site serine present: True'}
expected = {'PKS_ER0': 'ER configuration inconclusive',
'PKS_ER1': 'ER domain putatively catalyzing 2R-configuration product formation',
'PKS_ER2': 'ER configuration inconclusive'}
assert {dom.domain_id: message for dom, message in results} == expected