def test_p450(self, mocked_get, mocked_match):
mocked_match.return_value = True
for char in string.ascii_uppercase:
mocked_get.return_value = [DummyAlignment(char, {407: char})]
pairings = analysis.asp_p450_oxy(self.record)
assert pairings == [(char, "active site cysteine present: %s" % (char == "C"))]
# and an inconclusive
mocked_match.return_value = False
# values here don't matter
mocked_get.return_value = [DummyAlignment("incon", {})]
pairings = analysis.asp_p450_oxy(self.record)
assert pairings == [("incon", "active site cysteine inconclusive")]
def test_p450(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, {407: char})])
pairings = analysis.asp_p450_oxy(self.record)
assert pairings == [(char, "active site cysteine present: %s" % (char == "C"))]
# 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.asp_p450_oxy(self.record)
assert pairings == [("incon", "active site cysteine inconclusive")]
def test_p450(self):
mock("subprocessing.run_hmmpfam2",
returns=parse_hmmpfam_results("p450.output"))
results = analysis.asp_p450_oxy(self.record)
expected = {
'PFAM_p450_0': 'active site cysteine inconclusive',
'PFAM_p450_1': 'active site cysteine inconclusive'
}
assert {dom.domain_id: message for dom, message in results} == expected