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_attC(self):
integron = Integron("foo")
self.assertFalse(integron.has_attC())
just_one_attC = Integron("just_one_attC")
just_one_attC.add_attC(10, 100, 1, 1e-2, "intersection_tyr_intI")
self.assertTrue(just_one_attC.has_attC())
def test_has_attC(self):
integron = Integron("foo")
self.assertFalse(integron.has_attC())
just_one_attC = Integron("just_one_attC")
just_one_attC.add_attC(10, 100, 1, 1e-2, "intersection_tyr_intI")
self.assertTrue(just_one_attC.has_attC())
def test_add_attc(self):
id_replicon = "acba.007.p01.13"
data_attc_1 = {
"pos_beg": 10,
"pos_end": 100,
"strand": -1,
"evalue": 1.1e-07,
"type_elt": "attC",
"annotation": "attC",
"model": "attc_4",
"distance_2attC": np.nan
}
attc_1 = pd.DataFrame(data_attc_1,
columns=self.columns,
index=['attc_001'])
attc_1 = attc_1.astype(dtype=self.dtype)
integron = Integron(id_replicon)
integron.add_attC(attc_1.loc['attc_001', 'pos_beg'],
attc_1.loc['attc_001',
'pos_end'], attc_1.loc['attc_001',
'strand'],
attc_1.loc['attc_001',
'evalue'], attc_1.loc['attc_001',
'model'])
pdt.assert_frame_equal(attc_1, integron.attC)
integron_finder.SIZE_REPLICON = 3
attc_2 = pd.DataFrame(data_attc_1,
columns=self.columns,
index=['attc_002'])
attc_2 = attc_2.astype(dtype=self.dtype)
attc_2['pos_beg'] = attc_2['pos_beg'] + 100
attc_2['pos_end'] = attc_2['pos_end'] + 100
attc_2["distance_2attC"] = (attc_2.loc['attc_002', 'pos_beg'] - attc_1.loc['attc_001', 'pos_end']) % \
integron_finder.SIZE_REPLICON
attc = attc_1.append(attc_2)
integron.add_attC(attc_2.loc['attc_002', 'pos_beg'],
attc_2.loc['attc_002',
'pos_end'], attc_2.loc['attc_002',
'strand'],
attc_2.loc['attc_002',
'evalue'], attc_2.loc['attc_002',
'model'])
pdt.assert_frame_equal(attc, integron.attC)
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_attc(self):
id_replicon = "acba.007.p01.13"
data_attc = {"pos_beg" : 10,
"pos_end" : 100,
"strand" : -1,
"evalue" : 1.1e-07,
"type_elt" : "attC",
"annotation" : "attC",
"model" : "attc_4"}
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_attc["pos_beg"]]
tmp_df["pos_end"] = [data_attc["pos_end"]]
tmp_df["strand"] = [data_attc["strand"]]
tmp_df["evalue"] = [data_attc["evalue"]]
tmp_df["type_elt"] = "attC"
tmp_df["annotation"] = "attC"
tmp_df["model"] = [data_attc["model"]]
df = df.append(tmp_df, ignore_index=True)
sizes_cassettes = [np.nan]
df["distance_2attC"] = sizes_cassettes
df.index = ["attc_%03i" % int(j + 1) for j in df.index]
integron = Integron(id_replicon)
integron.add_attC(data_attc["pos_beg"],
data_attc["pos_end"],
data_attc["strand"],
data_attc["evalue"],
data_attc["model"])
self.assert_frame_equal(df, integron.attC, check_dtype=False)
self.assertListEqual(sizes_cassettes, integron.sizes_cassettes)
integron_finder.SIZE_REPLICON = 3
tmp_df2 = pd.DataFrame()
tmp_df2["pos_beg"] = [data_attc["pos_beg"] + 100]
tmp_df2["pos_end"] = [data_attc["pos_end"] + 100]
tmp_df2["strand"] = [data_attc["strand"]]
tmp_df2["evalue"] = [data_attc["evalue"]]
tmp_df2["type_elt"] = "attC"
tmp_df2["annotation"] = "attC"
tmp_df2["model"] = [data_attc["model"]]
sizes_cassettes.append((
(data_attc["pos_beg"] + 100) -
(data_attc["pos_end"])) %
integron_finder.SIZE_REPLICON)
df = df.append(tmp_df2, ignore_index=True)
df["distance_2attC"] = sizes_cassettes
df.index = ["attc_%03i" % int(j + 1) for j in df.index]
integron.add_attC(data_attc["pos_beg"] + 100,
data_attc["pos_end"] + 100,
data_attc["strand"],
data_attc["evalue"],
data_attc["model"])
self.assert_frame_equal(df, integron.attC, check_dtype=False)
self.assertListEqual(sizes_cassettes, integron.sizes_cassettes)
def test_add_attc(self):
id_replicon = "acba.007.p01.13"
data_attc = {
"pos_beg": 10,
"pos_end": 100,
"strand": -1,
"evalue": 1.1e-07,
"type_elt": "attC",
"annotation": "attC",
"model": "attc_4",
}
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_attc["pos_beg"]]
tmp_df["pos_end"] = [data_attc["pos_end"]]
tmp_df["strand"] = [data_attc["strand"]]
tmp_df["evalue"] = [data_attc["evalue"]]
tmp_df["type_elt"] = "attC"
tmp_df["annotation"] = "attC"
tmp_df["model"] = [data_attc["model"]]
df = df.append(tmp_df, ignore_index=True)
sizes_cassettes = [np.nan]
df["distance_2attC"] = sizes_cassettes
df.index = ["attc_%03i" % int(j + 1) for j in df.index]
integron = Integron(id_replicon)
integron.add_attC(
data_attc["pos_beg"], data_attc["pos_end"], data_attc["strand"], data_attc["evalue"], data_attc["model"]
)
self.assert_frame_equal(df, integron.attC, check_dtype=False)
self.assertListEqual(sizes_cassettes, integron.sizes_cassettes)
integron_finder.SIZE_REPLICON = 3
tmp_df2 = pd.DataFrame()
tmp_df2["pos_beg"] = [data_attc["pos_beg"] + 100]
tmp_df2["pos_end"] = [data_attc["pos_end"] + 100]
tmp_df2["strand"] = [data_attc["strand"]]
tmp_df2["evalue"] = [data_attc["evalue"]]
tmp_df2["type_elt"] = "attC"
tmp_df2["annotation"] = "attC"
tmp_df2["model"] = [data_attc["model"]]
sizes_cassettes.append(((data_attc["pos_beg"] + 100) - (data_attc["pos_end"])) % integron_finder.SIZE_REPLICON)
df = df.append(tmp_df2, ignore_index=True)
df["distance_2attC"] = sizes_cassettes
df.index = ["attc_%03i" % int(j + 1) for j in df.index]
integron.add_attC(
data_attc["pos_beg"] + 100,
data_attc["pos_end"] + 100,
data_attc["strand"],
data_attc["evalue"],
data_attc["model"],
)
self.assert_frame_equal(df, integron.attC, check_dtype=False)
self.assertListEqual(sizes_cassettes, integron.sizes_cassettes)
