def test_integron_1elem_prom(self):
"""
Test to_gbk when the only element is an integron composed of 1 promoter only.
"""
infos = {
"ID_replicon": "acba.007.p01.13",
"ID_integron": "integron_01",
"element": "Pc_int1",
"pos_beg": 25,
"pos_end": 51,
"strand": -1,
"evalue": np.nan,
"type_elt": "Promoter",
"annotation": "Pc_1",
"model": "NA",
"type": "complete",
"default": "Yes",
"distance_2attC": np.nan
}
df = pd.DataFrame(infos, index=[0])
start_seq = self.seq.seq
start_id = self.seq.id
integron_finder.to_gbk(df, self.seq)
# Check that there are 2 features (integron and promoter)
self.assertEqual(len(self.seq.features), 2)
# Check that initial sequence and id are not modified
self.assertEqual(self.seq.seq, start_seq)
self.assertEqual(self.seq.id, start_id)
# Check first feature: integron
self.assertEqual(self.seq.features[0].location.start,
infos["pos_beg"] - 1)
self.assertEqual(self.seq.features[0].location.end, infos["pos_end"])
self.assertEqual(self.seq.features[0].strand, 0)
self.assertEqual(self.seq.features[0].type, "integron")
self.assertEqual(self.seq.features[0].qualifiers["integron_id"],
infos["ID_integron"])
self.assertEqual(self.seq.features[0].qualifiers["integron_type"],
infos["type"])
# Check second feature: promotor
self.assertEqual(self.seq.features[1].location.start,
infos["pos_beg"] - 1)
self.assertEqual(self.seq.features[1].location.end, infos["pos_end"])
self.assertEqual(self.seq.features[1].strand, infos["strand"])
self.assertEqual(self.seq.features[1].type, infos["type_elt"])
self.assertEqual(self.seq.features[1].qualifiers["Promoter"],
infos["element"])
self.assertEqual(self.seq.features[1].qualifiers["model"],
infos["model"])
def test_integron_long_seqname(self):
"""
Test to_gbk when the only element is an integron composed of 1 protein only.
"""
infos = {
"ID_replicon": "acba.007.p01.13",
"ID_integron": "integron_01",
"element": "ACBA.007.P01_13_20",
"pos_beg": 17375,
"pos_end": 17375,
"strand": -1,
"evalue": np.nan,
"type_elt": "protein",
"annotation": "protein",
"model": "NA",
"type": "complete",
"default": "Yes",
"distance_2attC": np.nan
}
df = pd.DataFrame(infos, index=[0])
start_seq = self.seq.seq
start_id = self.seq.id
seq_name = self.seq.name
self.seq.name = "abcdefgh" + seq_name
integron_finder.to_gbk(df, self.seq)
# Translation should be protein ACBA.007.P01_13_20 in
# tests/data/Results_Integron_Finder_acba.007.p01.13/acba.007.p01.13.prt
translate = (
"MKGWLFLVIAIVGEVIATSALKSSEGFTKLAPSAVVIIGYGIAFYFLSLVLKSIPVGVAY"
"AVWSGLGVVIITAIAWLLHGQKLDAWGFVGMGLIIAAFLLARSPSWKSLRRPTPW*")
# Check that there are 2 features (integron and protein)
self.assertEqual(len(self.seq.features), 2)
# Check that initial sequence and id are not modified
self.assertEqual(self.seq.seq, start_seq)
self.assertEqual(self.seq.id, start_id)
# Check that sequence name has been shortened
self.assertEqual(self.seq.name, "h" + seq_name)
def test_integron_1elem_prot(self):
"""
Test to_gbk when the only element is an integron composed of 1 protein only.
"""
infos = {
"ID_replicon": "acba.007.p01.13",
"ID_integron": "integron_01",
"element": "ACBA.007.P01_13_20",
"pos_beg": 17375,
"pos_end": 17375,
"strand": -1,
"evalue": np.nan,
"type_elt": "protein",
"annotation": "protein",
"model": "NA",
"type": "complete",
"default": "Yes",
"distance_2attC": np.nan
}
df = pd.DataFrame(infos, index=[0])
start_seq = self.seq.seq
start_id = self.seq.id
integron_finder.to_gbk(df, self.seq)
# Translation should be protein ACBA.007.P01_13_20 in
# tests/data/Results_Integron_Finder_acba.007.p01.13/acba.007.p01.13.prt
translate = (
"MKGWLFLVIAIVGEVIATSALKSSEGFTKLAPSAVVIIGYGIAFYFLSLVLKSIPVGVAY"
"AVWSGLGVVIITAIAWLLHGQKLDAWGFVGMGLIIAAFLLARSPSWKSLRRPTPW*")
# Check that there are 2 features (integron and protein)
self.assertEqual(len(self.seq.features), 2)
# Check that initial sequence and id are not modified
self.assertEqual(self.seq.seq, start_seq)
self.assertEqual(self.seq.id, start_id)
# Check first feature: integron
self.assertEqual(self.seq.features[0].location.start,
infos["pos_beg"] - 1)
self.assertEqual(self.seq.features[0].location.end, infos["pos_end"])
self.assertEqual(self.seq.features[0].strand, 0)
self.assertEqual(self.seq.features[0].type, "integron")
self.assertEqual(self.seq.features[0].qualifiers["integron_id"],
infos["ID_integron"])
self.assertEqual(self.seq.features[0].qualifiers["integron_type"],
infos["type"])
# Check second feature: protein
self.assertEqual(self.seq.features[1].location.start,
infos["pos_beg"] - 1)
self.assertEqual(self.seq.features[1].location.end, infos["pos_end"])
self.assertEqual(self.seq.features[1].strand, infos["strand"])
self.assertEqual(self.seq.features[1].type, "CDS")
self.assertEqual(self.seq.features[1].qualifiers["protein_id"],
infos["element"])
self.assertEqual(self.seq.features[1].qualifiers["gene"],
infos["annotation"])
self.assertEqual(self.seq.features[1].qualifiers["model"],
infos["model"])
self.assertEqual(
self.seq.features[1].qualifiers["translation"].tostring(),
translate)
def test_integron_2int_nelem(self):
"""
Test to_gbk when there are 2 integrons:
integron 1 with several elements: protein, integrase, promoter
integron 2 with only 1 attC site
Integrons are not over the edge of sequence
"""
# integron 1
int_id = "integron_01"
rep_id = "acba.007.p01.13"
int_type = "complete"
infos_prom = {
"ID_replicon": rep_id,
"ID_integron": int_id,
"element": "Pc_int1",
"pos_beg": 25,
"pos_end": 51,
"strand": -1,
"evalue": np.nan,
"type_elt": "Promoter",
"annotation": "Pc_1",
"model": "NA",
"type": int_type,
"default": "Yes",
"distance_2attC": np.nan
}
infos_int = {
"ID_replicon": rep_id,
"ID_integron": int_id,
"element": "ACBA.007.P01_13_1",
"pos_beg": 55,
"pos_end": 1014,
"strand": 1,
"evalue": 1.9e-25,
"type_elt": "protein",
"annotation": "intI",
"model": "NA",
"type": int_type,
"default": "Yes",
"distance_2attC": np.nan
}
infos_prot = {
"ID_replicon": rep_id,
"ID_integron": int_id,
"element": "ACBA.007.P01_13_20",
"pos_beg": 2000,
"pos_end": 2056,
"strand": -1,
"evalue": np.nan,
"type_elt": "protein",
"annotation": "protein",
"model": "intersection_tyr_intI",
"type": int_type,
"default": "Yes",
"distance_2attC": np.nan
}
# integron 2
infos_attC = {
"ID_replicon": rep_id,
"ID_integron": "integron_02",
"element": "attc_001",
"pos_beg": 17825,
"pos_end": 17884,
"strand": -1,
"evalue": 1e-9,
"type_elt": "attC",
"annotation": "attC",
"model": "attc_4",
"type": int_type,
"default": "Yes",
"distance_2attC": np.nan
}
df1 = pd.DataFrame(infos_prom, index=[0])
df2 = pd.DataFrame(infos_int, index=[0])
df3 = pd.DataFrame(infos_prot, index=[0])
df4 = pd.DataFrame(infos_attC, index=[0])
df = pd.concat([df1, df2, df3, df4])
start_seq = self.seq.seq
start_id = self.seq.id
lenseq = len(self.seq)
tr_int = (
"MKTATAPLPPLRSVKVLDQLRERIRYLHYSLRTEQAYVNWVRAFIRFHGVRHPATLGSSE"
"VEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEIGRPRPSRRLPVVLTPD"
"EVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALML"
"PESLAPSLREQLSRARAWWLKDQAEGRSGVALPDALERKYPRAGHSWPWFWVFAQHTHST"
"DPRSGVVRRHHMYDQTFQRAFKRAVEGTVAKLAMRQPFVLFKGLTFQKLCLPGAFRPGDH"
"HNKMLRPGLCVVHASPQYL*")
tr_prot = (
"MKGWLFLVIAIVGEVIATSALKSSEGFTKLAPSAVVIIGYGIAFYFLSLVLKSIPVGVAY"
"AVWSGLGVVIITAIAWLLHGQKLDAWGFVGMGLIIAAFLLARSPSWKSLRRPTPW*")
integron_finder.to_gbk(df, self.seq)
# Check that there are 6 features (integron1, promoter, integrase, protein,
# integron2, attC)
self.assertEqual(len(self.seq.features), 6)
# Check that initial sequence and id are not modified
self.assertEqual(self.seq.seq, start_seq)
self.assertEqual(self.seq.id, start_id)
# Check first feature: integron1
self.assertEqual(self.seq.features[0].location.start,
infos_prom["pos_beg"] - 1)
self.assertEqual(self.seq.features[0].location.end,
infos_prot["pos_end"])
self.assertEqual(self.seq.features[0].strand, 0)
self.assertEqual(self.seq.features[0].type, "integron")
self.assertEqual(self.seq.features[0].qualifiers["integron_id"],
int_id)
self.assertEqual(self.seq.features[0].qualifiers["integron_type"],
int_type)
# Check feature 2: promoter
self.assertEqual(self.seq.features[1].location.start,
infos_prom["pos_beg"] - 1)
self.assertEqual(self.seq.features[1].location.end,
infos_prom["pos_end"])
self.assertEqual(self.seq.features[1].strand, infos_prom["strand"])
self.assertEqual(self.seq.features[1].type, "Promoter")
self.assertEqual(self.seq.features[1].qualifiers["Promoter"],
infos_prom["element"])
self.assertEqual(self.seq.features[1].qualifiers["model"],
infos_prom["model"])
# Check feature 3: integrase
self.assertEqual(self.seq.features[2].location.start,
infos_int["pos_beg"] - 1)
self.assertEqual(self.seq.features[2].location.end,
infos_int["pos_end"])
self.assertEqual(self.seq.features[2].strand, infos_int["strand"])
self.assertEqual(self.seq.features[2].type, "integrase")
self.assertEqual(self.seq.features[2].qualifiers["protein_id"],
infos_int["element"])
self.assertEqual(self.seq.features[2].qualifiers["gene"],
infos_int["annotation"])
self.assertEqual(self.seq.features[2].qualifiers["model"],
infos_int["model"])
self.assertEqual(
self.seq.features[2].qualifiers["translation"].tostring(), tr_int)
# Check feature 4: protein
self.assertEqual(self.seq.features[3].location.start,
infos_prot["pos_beg"] - 1)
self.assertEqual(self.seq.features[3].location.end,
infos_prot["pos_end"])
self.assertEqual(self.seq.features[3].strand, infos_prot["strand"])
self.assertEqual(self.seq.features[3].type, "CDS")
self.assertEqual(self.seq.features[3].qualifiers["protein_id"],
infos_prot["element"])
self.assertEqual(self.seq.features[3].qualifiers["gene"],
infos_prot["annotation"])
self.assertEqual(self.seq.features[3].qualifiers["model"],
infos_prot["model"])
self.assertEqual(
self.seq.features[3].qualifiers["translation"].tostring(), tr_prot)
# Check feature 5: integron2
self.assertEqual(self.seq.features[4].location.start,
infos_attC["pos_beg"] - 1)
self.assertEqual(self.seq.features[4].location.end,
infos_attC["pos_end"])
self.assertEqual(self.seq.features[4].strand, 0)
self.assertEqual(self.seq.features[4].type, "integron")
self.assertEqual(self.seq.features[4].qualifiers["integron_id"],
"integron_02")
self.assertEqual(self.seq.features[4].qualifiers["integron_type"],
int_type)
# Check feature 6: attC
self.assertEqual(self.seq.features[5].location.start,
infos_attC["pos_beg"] - 1)
self.assertEqual(self.seq.features[5].location.end,
infos_attC["pos_end"])
self.assertEqual(self.seq.features[5].strand, infos_attC["strand"])
self.assertEqual(self.seq.features[5].type, "attC")
self.assertEqual(self.seq.features[5].qualifiers["attC"],
infos_attC["element"])
self.assertEqual(self.seq.features[5].qualifiers["model"],
infos_attC["model"])
def test_integron_1elem_int(self):
"""
Test to_gbk when the only element is an integron composed of 1 integrase only.
"""
infos = {
"ID_replicon": "acba.007.p01.13",
"ID_integron": "integron_01",
"element": "ACBA.007.P01_13_1",
"pos_beg": 55,
"pos_end": 1014,
"strand": 1,
"evalue": 1.9e-25,
"type_elt": "protein",
"annotation": "intI",
"model": "intersection_tyr_intI",
"type": "complete",
"default": "Yes",
"distance_2attC": np.nan
}
df = pd.DataFrame(infos, index=[0])
start_seq = self.seq.seq
start_id = self.seq.id
integron_finder.to_gbk(df, self.seq)
# Translation should be protein ACBA.007.P01_13_1 in
# tests/data/Results_Integron_Finder_acba.007.p01.13/acba.007.p01.13.prt
translate = (
"MKTATAPLPPLRSVKVLDQLRERIRYLHYSLRTEQAYVNWVRAFIRFHGVRHPATLGSSE"
"VEAFLSWLANERKVSVSTHRQALAALLFFYGKVLCTDLPWLQEIGRPRPSRRLPVVLTPD"
"EVVRILGFLEGEHRLFAQLLYGTGMRISEGLQLRVKDLDFDHGTIIVREGKGSKDRALML"
"PESLAPSLREQLSRARAWWLKDQAEGRSGVALPDALERKYPRAGHSWPWFWVFAQHTHST"
"DPRSGVVRRHHMYDQTFQRAFKRAVEGTVAKLAMRQPFVLFKGLTFQKLCLPGAFRPGDH"
"HNKMLRPGLCVVHASPQYL*")
# Check that there are 2 features (integron and protein)
self.assertEqual(len(self.seq.features), 2)
# Check that initial sequence and id are not modified
self.assertEqual(self.seq.seq, start_seq)
self.assertEqual(self.seq.id, start_id)
# Check first feature: integron
self.assertEqual(self.seq.features[0].location.start,
infos["pos_beg"] - 1)
self.assertEqual(self.seq.features[0].location.end, infos["pos_end"])
self.assertEqual(self.seq.features[0].strand, 0)
self.assertEqual(self.seq.features[0].type, "integron")
self.assertEqual(self.seq.features[0].qualifiers["integron_id"],
infos["ID_integron"])
self.assertEqual(self.seq.features[0].qualifiers["integron_type"],
infos["type"])
# Check second feature: protein
self.assertEqual(self.seq.features[1].location.start,
infos["pos_beg"] - 1)
self.assertEqual(self.seq.features[1].location.end, infos["pos_end"])
self.assertEqual(self.seq.features[1].strand, infos["strand"])
self.assertEqual(self.seq.features[1].type, "integrase")
self.assertEqual(self.seq.features[1].qualifiers["protein_id"],
infos["element"])
self.assertEqual(self.seq.features[1].qualifiers["gene"],
infos["annotation"])
self.assertEqual(self.seq.features[1].qualifiers["model"],
infos["model"])
self.assertEqual(
self.seq.features[1].qualifiers["translation"].tostring(),
translate)