def test_add_integrase(self): id_replicon = "acba.007.p01.13" data_integrase = { "pos_beg": 55, "pos_end": 1014, "strand": 1, "evalue": 1.900000e-25, "type_elt": "protein", "annotation": "intI", "model": "intersection_tyr_intI", "distance_2attC": np.nan } id_int = "ACBA.007.P01_13_1" df = pd.DataFrame(data_integrase, columns=self.columns, index=[id_int]) df = df.astype(dtype=self.dtype) integron = Integron(id_replicon) integron.add_integrase(data_integrase["pos_beg"], data_integrase["pos_end"], id_int, data_integrase["strand"], data_integrase["evalue"], data_integrase["model"]) pdt.assert_frame_equal(df, integron.integrase) with self.assertRaises(RuntimeError) as ctx: integron.add_integrase(data_integrase["pos_beg"], data_integrase["pos_end"], id_int, data_integrase["strand"], data_integrase["evalue"], data_integrase["model"]) self.assertEqual(str(ctx.exception), "add_integrase should be called once.")
def test_type(self): no_integrase = Integron("foo") self.assertIsNone(no_integrase.type()) just_one_integrase = Integron("just_one_integrase") just_one_integrase.add_integrase(10, 100, 'foo', 1, 1e-2, "intersection_tyr_intI") self.assertEqual(just_one_integrase.type(), "In0") just_one_attC = Integron("just_one_attC") just_one_attC.add_attC(10, 100, 1, 1e-2, "intersection_tyr_intI") self.assertEqual(just_one_attC.type(), "attC0") one_integrase_one_attC = Integron("one_integrase_one_attC") one_integrase_one_attC.add_integrase(10, 100, 'foo', 1, 1e-2, "intersection_tyr_intI") one_integrase_one_attC.add_attC(10, 100, 1, 1e-2, "intersection_tyr_intI") self.assertEqual(one_integrase_one_attC.type(), "complete")
def test_has_integrase(self): integron = Integron("foo") self.assertFalse(integron.has_integrase()) just_one_integrase = Integron("just_one_integrase") just_one_integrase.add_integrase(10, 100, "foo", 1, 1e-2, "intersection_tyr_intI") self.assertTrue(just_one_integrase.has_integrase())
def test_has_integrase(self): integron = Integron("foo") self.assertFalse(integron.has_integrase()) just_one_integrase = Integron("just_one_integrase") just_one_integrase.add_integrase(10, 100, 'foo', 1, 1e-2, "intersection_tyr_intI") self.assertTrue(just_one_integrase.has_integrase())
def test_type(self): no_integrase = Integron("foo") self.assertIsNone(no_integrase.type()) just_one_integrase = Integron("just_one_integrase") just_one_integrase.add_integrase(10, 100, "foo", 1, 1e-2, "intersection_tyr_intI") self.assertEqual(just_one_integrase.type(), "In0") just_one_attC = Integron("just_one_attC") just_one_attC.add_attC(10, 100, 1, 1e-2, "intersection_tyr_intI") self.assertEqual(just_one_attC.type(), "attC0") one_integrase_one_attC = Integron("one_integrase_one_attC") one_integrase_one_attC.add_integrase(10, 100, "foo", 1, 1e-2, "intersection_tyr_intI") one_integrase_one_attC.add_attC(10, 100, 1, 1e-2, "intersection_tyr_intI") self.assertEqual(one_integrase_one_attC.type(), "complete")
def test_add_integrase(self): # pos_beg, pos_end, strand, evalue, type_elt, annotation, model, distance_2attC # ACBA.007.P01_13_1, 55 , 1014, 1, 1.900000e-25, protein, intI, intersection_tyr_intI, NaN # LIAN.001.C02_10_825, 934165 , 934689, -1, 1.900000e-26, protein, intI, intersection_tyr_intI, NaN # PSSU.001.C01_13_1919, 2131128, 2132135, 1, 5.100000e-27, protein, intI, intersection_tyr_intI, NaN id_replicon = "acba.007.p01.13" data_integrase = { "pos_beg": 55, "pos_end": 1014, "strand": 1, "evalue": 1.900000e-25, "type_elt": "protein", "annotation": "intI", "model": "intersection_tyr_intI", "distance_2attC": np.nan, } id_int = "ACBA.007.P01_13_1" df = pd.DataFrame( columns=["pos_beg", "pos_end", "strand", "evalue", "type_elt", "model", "distance_2attC", "annotation"] ) tmp_df = pd.DataFrame() tmp_df["pos_beg"] = [data_integrase["pos_beg"]] tmp_df["pos_end"] = [data_integrase["pos_end"]] tmp_df["strand"] = [data_integrase["strand"]] tmp_df["evalue"] = [data_integrase["evalue"]] tmp_df["type_elt"] = data_integrase["type_elt"] tmp_df["annotation"] = data_integrase["annotation"] tmp_df["model"] = [data_integrase["model"]] tmp_df.index = [id_int] tmp_df["distance_2attC"] = [np.nan] df = df.append(tmp_df) integron = Integron(id_replicon) integron.add_integrase( data_integrase["pos_beg"], data_integrase["pos_end"], [id_int], data_integrase["strand"], data_integrase["evalue"], data_integrase["model"], ) self.assert_frame_equal(df, integron.integrase, check_dtype=False)
def test_add_integrase(self): # pos_beg, pos_end, strand, evalue, type_elt, annotation, model, distance_2attC # ACBA.007.P01_13_1, 55 , 1014, 1, 1.900000e-25, protein, intI, intersection_tyr_intI, NaN # LIAN.001.C02_10_825, 934165 , 934689, -1, 1.900000e-26, protein, intI, intersection_tyr_intI, NaN # PSSU.001.C01_13_1919, 2131128, 2132135, 1, 5.100000e-27, protein, intI, intersection_tyr_intI, NaN id_replicon = "acba.007.p01.13" data_integrase = { "pos_beg": 55, "pos_end": 1014, "strand": 1, "evalue": 1.900000e-25, "type_elt": "protein", "annotation": "intI", "model": "intersection_tyr_intI", "distance_2attC": np.nan } id_int = "ACBA.007.P01_13_1" df = pd.DataFrame(columns=[ "pos_beg", "pos_end", "strand", "evalue", "type_elt", "model", "distance_2attC", "annotation" ]) tmp_df = pd.DataFrame() tmp_df["pos_beg"] = [data_integrase["pos_beg"]] tmp_df["pos_end"] = [data_integrase["pos_end"]] tmp_df["strand"] = [data_integrase["strand"]] tmp_df["evalue"] = [data_integrase["evalue"]] tmp_df["type_elt"] = data_integrase["type_elt"] tmp_df["annotation"] = data_integrase["annotation"] tmp_df["model"] = [data_integrase["model"]] tmp_df.index = [id_int] tmp_df["distance_2attC"] = [np.nan] df = df.append(tmp_df) integron = Integron(id_replicon) integron.add_integrase(data_integrase["pos_beg"], data_integrase["pos_end"], [id_int], data_integrase["strand"], data_integrase["evalue"], data_integrase["model"]) self.assert_frame_equal(df, integron.integrase, check_dtype=False)