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)
