def test_integrons_report(self):
replicon_name = "acba.007.p01.13"
replicon_path = self.find_data(
os.path.join('Replicons', replicon_name + '.fst'))
topologies = Topology('circ')
with FastaIterator(replicon_path) as sequences_db:
sequences_db.topologies = topologies
replicon = next(sequences_db)
args = argparse.Namespace()
cfg = Config(args)
cfg._args.eagle_eyes = False
cfg._args.eagle_eyes = False
cfg._args.local_max = False
integron = Integron(replicon, cfg)
columns = [
'pos_beg', 'pos_end', 'strand', 'evalue', 'type_elt', 'model',
'distance_2attC', 'annotation'
]
dtype = {
"pos_beg": 'int',
"pos_end": 'int',
"strand": 'int',
"evalue": 'float',
"type_elt": 'str',
"annotation": 'str',
"model": 'str',
"distance_2attC": 'float'
}
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"
integrase = pd.DataFrame(data_integrase,
columns=columns,
index=[id_int])
integrase = integrase.astype(dtype=dtype)
data_attc = {
"pos_beg": [17825, 19080, 19618],
"pos_end": [17884, 19149, 19726],
"strand": [-1] * 3,
"evalue": [1.000000e-09, 1.000000e-04, 1.100000e-07],
"type_elt": ["attC"] * 3,
"annotation": ["attC"] * 3,
"model": ["attc_4"] * 3,
"distance_2attC": [np.nan, 1196.0, 469.0]
}
attC = pd.DataFrame(data_attc,
columns=columns,
index=['attc_00{}'.format(i) for i in range(1, 4)])
attC = attC.astype(dtype=dtype)
promoter = pd.DataFrame(
{
'pos_beg': 25,
'pos_end': 51,
'strand': -1,
'evalue': np.nan,
'type_elt': 'Promoter',
'annotation': 'Pc_1',
'model': np.nan,
'distance_2attC': np.nan
},
index=['Pc_int1'],
columns=columns)
promoter = promoter.astype(dtype=dtype)
proteins = pd.DataFrame(
{
'pos_beg': [17375, 17886, 19090, 19721],
'pos_end': [17722, 18665, 19749, 20254],
'strand': [-1] * 4,
'evalue': [np.nan] * 4,
'type_elt': ['protein'] * 4,
'annotation': ['protein'] * 4,
'model': [np.nan] * 4,
'distance_2attC': [np.nan] * 4
},
index=['ACBA.007.P01_13_2{}'.format(i) for i in range(0, 4)],
columns=columns)
proteins = proteins.astype(dtype=dtype)
integron.integrase = integrase
integron.attC = attC
integron.promoter = promoter
integron.proteins = proteins
report = results.integrons_report([integron])
exp_report = pd.read_csv(self.find_data(
os.path.join('Results_Integron_Finder_{}'.format(replicon_name),
'{}.integrons'.format(replicon_name))),
sep="\t")
exp_report = exp_report.astype(dtype=dtype)
pdt.assert_frame_equal(exp_report, report)
def test_integrons_report(self):
replicon_name = "acba.007.p01.13"
replicon_path = self.find_data(os.path.join('Replicons', replicon_name + '.fst'))
topologies = Topology('circ')
with FastaIterator(replicon_path) as sequences_db:
sequences_db.topologies = topologies
replicon = next(sequences_db)
args = argparse.Namespace()
cfg = Config(args)
cfg._args.eagle_eyes = False
cfg._args.eagle_eyes = False
cfg._args.local_max = False
integron = Integron(replicon, cfg)
columns = ['pos_beg', 'pos_end', 'strand', 'evalue', 'type_elt', 'model', 'distance_2attC', 'annotation']
dtype = {"pos_beg": 'int',
"pos_end": 'int',
"strand": 'int',
"evalue": 'float',
"type_elt": 'str',
"annotation": 'str',
"model": 'str',
"distance_2attC": 'float'}
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"
integrase = pd.DataFrame(data_integrase, columns=columns, index=[id_int])
integrase = integrase.astype(dtype=dtype)
data_attc = {"pos_beg": [17825, 19080, 19618],
"pos_end": [17884, 19149, 19726],
"strand": [-1] * 3,
"evalue": [1.000000e-09, 1.000000e-04, 1.100000e-07],
"type_elt": ["attC"] * 3,
"annotation": ["attC"] * 3,
"model": ["attc_4"] * 3,
"distance_2attC": [np.nan, 1196.0, 469.0]}
attC = pd.DataFrame(data_attc,
columns=columns,
index=['attc_00{}'.format(i) for i in range(1, 4)])
attC = attC.astype(dtype=dtype)
promoter = pd.DataFrame({'pos_beg': 25,
'pos_end': 51,
'strand': -1,
'evalue': np.nan,
'type_elt': 'Promoter',
'annotation': 'Pc_1',
'model': np.nan,
'distance_2attC': np.nan
},
index=['Pc_int1'],
columns=columns
)
promoter = promoter.astype(dtype=dtype)
proteins = pd.DataFrame({'pos_beg': [17375, 17886, 19090, 19721],
'pos_end': [17722, 18665, 19749, 20254],
'strand': [-1] * 4,
'evalue': [np.nan] * 4,
'type_elt': ['protein'] * 4,
'annotation': ['protein'] * 4,
'model': [np.nan] * 4,
'distance_2attC': [np.nan] * 4
},
index=['ACBA.007.P01_13_2{}'.format(i) for i in range(0, 4)],
columns=columns
)
proteins = proteins.astype(dtype=dtype)
integron.integrase = integrase
integron.attC = attC
integron.promoter = promoter
integron.proteins = proteins
report = results.integrons_report([integron])
exp_report = pd.read_csv(
self.find_data(os.path.join('Results_Integron_Finder_{}'.format(replicon_name),
'{}.integrons'.format(replicon_name)
)),
sep="\t"
)
exp_report = exp_report.astype(dtype=dtype)
pdt.assert_frame_equal(exp_report, report)
def test_describe(self):
replicon_name = "acba.007.p01.13"
replicon_path = self.find_data(
os.path.join('Replicons', replicon_name + '.fst'))
topologies = Topology('lin')
with FastaIterator(replicon_path) as sequences_db:
sequences_db.topologies = topologies
replicon = next(sequences_db)
args = argparse.Namespace()
args.eagle_eyes = False
args.local_max = False
cfg = Config(args)
integron = Integron(replicon, cfg)
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"
integrase = pd.DataFrame(data_integrase,
columns=self.columns,
index=[id_int])
integrase = integrase.astype(dtype=self.dtype)
data_attc = {
"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 = pd.DataFrame(data_attc,
columns=self.columns,
index=['attc_001'])
attC = attC.astype(dtype=self.dtype)
promoter = pd.DataFrame(data_attc,
columns=self.columns,
index=['prom_001'])
promoter = promoter.astype(dtype=self.dtype)
attI = pd.DataFrame(data_attc,
columns=self.columns,
index=['attI_001'])
attI = attI.astype(dtype=self.dtype)
proteins = pd.DataFrame(data_attc,
columns=self.columns,
index=['prot_001'])
proteins = proteins.astype(dtype=self.dtype)
excp_description = pd.concat(
[integrase, attC, promoter, attI, proteins], ignore_index=False)
excp_description = excp_description.reset_index()
excp_description.columns = ["element"] + list(
excp_description.columns[1:])
excp_description["type"] = "complete"
excp_description["ID_replicon"] = replicon.id
excp_description["ID_integron"] = id(
integron) # uniq identifier of a given Integron
excp_description["default"] = "Yes"
excp_description["considered_topology"] = replicon.topology
excp_description.drop_duplicates(subset=["element"], inplace=True)
self.cfg._args.eagle_eyes = False
self.cfg._args.eagle_eyes = False
integron.integrase = integrase
integron.attC = attC
integron.promoter = promoter
integron.attI = attI
integron.proteins = proteins
recieved_description = integron.describe()
pdt.assert_frame_equal(recieved_description, excp_description)