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