def test_filter_evalue_thres(self):
"""
Test that the filter by a maximum attc size works.
"""
filename = self.find_data(
os.path.join(
"Results_Integron_Finder_{}".format(self.replicon_name),
"tmp_{}".format(self.replicon_id),
"{}_attc_table.res".format(self.replicon_id)))
df = infernal.read_infernal(filename,
self.replicon_id,
self.length_cm,
evalue=1e-8)
expect = pd.DataFrame(columns=[
"Accession_number", "cm_attC", "cm_debut", "cm_fin", "pos_beg",
"pos_end", "sens", "evalue"
])
expect = expect.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 17825,
"pos_end": 17884,
"sens": "-",
"evalue": 1e-9
},
ignore_index=True)
expect = expect.astype(self.dtype)
pdt.assert_frame_equal(df, expect)
def test_no_total_cm_match_strandm(self):
"""
Test that when the model did not completely match on the sequence,
the start and end positions of hit are well recalculated. All hits are on strand -
"""
filename = self.find_data(
os.path.join("fictive_results", "{}_attc_table-partialm.res".format(self.replicon_id)))
df = infernal.read_infernal(filename, self.replicon_id, self.length_cm)
expect = pd.DataFrame(columns=["Accession_number", "cm_attC", "cm_debut",
"cm_fin", "pos_beg", "pos_end", "sens", "evalue"])
expect = expect.append({"Accession_number": self.replicon_id, "cm_attC": "attC_4",
"cm_debut": 1, "cm_fin": 40, "pos_beg": 17818,
"pos_end": 17884, "sens": "-", "evalue": 1e-9},
ignore_index=True)
expect = expect.append({"Accession_number": self.replicon_id, "cm_attC": "attC_4",
"cm_debut": 1, "cm_fin": 47, "pos_beg": 19080,
"pos_end": 19149, "sens": "-", "evalue": 1e-4},
ignore_index=True)
expect = expect.append({"Accession_number": self.replicon_id, "cm_attC": "attC_4",
"cm_debut": 10, "cm_fin": 47, "pos_beg": 19618,
"pos_end": 19735, "sens": "-", "evalue": 1.1e-7},
ignore_index=True)
# convert positions to int
intcols = ["cm_debut", "cm_fin", "pos_beg", "pos_end"]
expect[intcols] = expect[intcols].astype(int)
pdt.assert_frame_equal(df, expect)
def test_generate_df(self):
"""
Test that if the infernal file exists and there are hits, it returns the
dataframe corresponding to it.
"""
filename = self.find_data(os.path.join("Results_Integron_Finder_{}".format(self.replicon_name),
"tmp_{}".format(self.replicon_id),
"{}_attc_table.res".format(self.replicon_id)))
df = infernal.read_infernal(filename, self.replicon_id, self.length_cm)
expect = pd.DataFrame(columns=["Accession_number", "cm_attC", "cm_debut",
"cm_fin", "pos_beg", "pos_end", "sens", "evalue"])
expect = expect.append({"Accession_number": self.replicon_id, "cm_attC": "attC_4",
"cm_debut": 1, "cm_fin": 47, "pos_beg": 17825,
"pos_end": 17884, "sens": "-", "evalue": 1e-9},
ignore_index=True)
expect = expect.append({"Accession_number": self.replicon_id, "cm_attC": "attC_4",
"cm_debut": 1, "cm_fin": 47, "pos_beg": 19080,
"pos_end": 19149, "sens": "-", "evalue": 1e-4},
ignore_index=True)
expect = expect.append({"Accession_number": self.replicon_id, "cm_attC": "attC_4",
"cm_debut": 1, "cm_fin": 47, "pos_beg": 19618,
"pos_end": 19726, "sens": "-", "evalue": 1.1e-7},
ignore_index=True)
# convert positions to int
intcols = ["cm_debut", "cm_fin", "pos_beg", "pos_end"]
expect[intcols] = expect[intcols].astype(int)
pdt.assert_frame_equal(df, expect)
def test_nohit(self):
"""
Test that if the infernal file exists but there is no hit
inside, it returns an empty dataframe.
"""
filename = self.find_data(os.path.join("fictive_results", "{}_attc_table-empty.res".format(self.replicon_id)))
df = infernal.read_infernal(filename, self.replicon_id, self.length_cm)
expect = pd.DataFrame(columns=["Accession_number", "cm_attC", "cm_debut",
"cm_fin", "pos_beg", "pos_end", "sens", "evalue"])
pdt.assert_frame_equal(df, expect)
def test_nofile(self):
"""
Test that the function returns an empty dataframe if the given infernal file does not
exist.
"""
filename = "infernal.txt"
df = infernal.read_infernal(filename, self.replicon_id, self.length_cm)
expect = pd.DataFrame(columns=["Accession_number", "cm_attC", "cm_debut",
"cm_fin", "pos_beg", "pos_end", "sens", "evalue"])
pdt.assert_frame_equal(df, expect)
def test_evalue_thres(self):
"""
Test that if the infernal file exists and there are hits, but
the given evalue threshold is smaller than the hits thresholds:
no hit kept, should return an empty dataframe.
"""
filename = self.find_data(os.path.join("Results_Integron_Finder_{}".format(self.replicon_name),
"tmp_{}".format(self.replicon_id),
"{}_attc_table.res".format(self.replicon_id)))
df = infernal.read_infernal(filename, self.replicon_id, self.length_cm, evalue=1e-10)
expect = pd.DataFrame(columns=["Accession_number", "cm_attC", "cm_debut",
"cm_fin", "pos_beg", "pos_end", "sens", "evalue"])
pdt.assert_frame_equal(df, expect)
def test_search_attc_empty(self):
"""
Test that when there are no attC sites detected, the attc array is empty.
"""
attc_file = self.find_data(
os.path.join("fictive_results",
self.replicon_id + "_attc_table-empty.res"))
# Construct attC dataframe (read from infernal file)
attc_df = infernal.read_infernal(attc_file, self.replicon_id,
self.length_cm)
attc_array = attc.search_attc(attc_df, True, self.dist_threshold,
self.replicon_size)
self.assertEqual(len(attc_array), 0)
attc_res = []
self.assertEqual(attc_array, attc_res)
def test_filter_evalue_thres(self):
"""
Test that the filter by a maximum attc size works.
"""
filename = self.find_data(os.path.join("Results_Integron_Finder_{}".format(self.replicon_name),
"tmp_{}".format(self.replicon_id),
"{}_attc_table.res".format(self.replicon_id)))
df = infernal.read_infernal(filename, self.replicon_id, self.length_cm, evalue=1e-8)
expect = pd.DataFrame(columns=["Accession_number", "cm_attC", "cm_debut",
"cm_fin", "pos_beg", "pos_end", "sens", "evalue"])
expect = expect.append({"Accession_number": self.replicon_id, "cm_attC": "attC_4",
"cm_debut": 1, "cm_fin": 47, "pos_beg": 17825,
"pos_end": 17884, "sens": "-", "evalue": 1e-9},
ignore_index=True)
# convert positions to int
intcols = ["cm_debut", "cm_fin", "pos_beg", "pos_end"]
expect[intcols] = expect[intcols].astype(int)
pdt.assert_frame_equal(df, expect)
def test_attcsize_minthres(self):
"""
Test that the filter by a minimum attc size works.
"""
filename = self.find_data(os.path.join("Results_Integron_Finder_{}".format(self.replicon_name),
"tmp_{}".format(self.replicon_id),
"{}_attc_table.res".format(self.replicon_id)))
df = infernal.read_infernal(filename, self.replicon_id, self.length_cm, size_min_attc=60)
expect = pd.DataFrame(columns=["Accession_number", "cm_attC", "cm_debut",
"cm_fin", "pos_beg", "pos_end", "sens", "evalue"])
expect = expect.append({"Accession_number": self.replicon_id, "cm_attC": "attC_4",
"cm_debut": 1, "cm_fin": 47, "pos_beg": 19080,
"pos_end": 19149, "sens": "-", "evalue": 1e-4},
ignore_index=True)
expect = expect.append({"Accession_number": self.replicon_id, "cm_attC": "attC_4",
"cm_debut": 1, "cm_fin": 47, "pos_beg": 19618,
"pos_end": 19726, "sens": "-", "evalue": 1.1e-7},
ignore_index=True)
# convert positions to int
intcols = ["cm_debut", "cm_fin", "pos_beg", "pos_end"]
expect[intcols] = expect[intcols].astype(int)
pdt.assert_frame_equal(df, expect)
def test_search_attc_uniq(self):
"""
Test that it finds a unique attc array when giving a table with 3 attC sites
on the same strand and separated by less than 4kb each.
"""
attc_file = self.find_data(
os.path.join(
"Results_Integron_Finder_{}".format(self.replicon_name),
"tmp_{}".format(self.replicon_id),
"{}_attc_table.res".format(self.replicon_id)))
# Construct attC dataframe (read from infernal file)
attc_df = infernal.read_infernal(attc_file, self.replicon_id,
self.length_cm)
# search attC arrays, keeping palindromes
# 2 attc sites are in the same array if they are on the same strand, and separated by
# a distance less than 4kb
attc_array = attc.search_attc(attc_df, True, self.dist_threshold,
self.replicon_size)
self.assertEqual(len(attc_array), 1)
# Construct expected output:
attc_res = pd.DataFrame(columns=[
"Accession_number", "cm_attC", "cm_debut", "cm_fin", "pos_beg",
"pos_end", "sens", "evalue"
],
dtype='int')
attc_res = attc_res.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 17825,
"pos_end": 17884,
"sens": "-",
"evalue": 1e-9
},
ignore_index=True)
attc_res = attc_res.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 19080,
"pos_end": 19149,
"sens": "-",
"evalue": 1e-4
},
ignore_index=True)
attc_res = attc_res.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 19618,
"pos_end": 19726,
"sens": "-",
"evalue": 1.1e-7
},
ignore_index=True)
# convert positions to int
intcols = ["cm_debut", "cm_fin", "pos_beg", "pos_end"]
attc_res[intcols] = attc_res[intcols].astype(int)
pdt.assert_frame_equal(attc_res, attc_array[0])
def test_search_attc_dist_diff_strand(self):
"""
Test that it finds a size 3 attc array when giving a table with:
- 3 attC sites on the same strand (-) and separated by less than 4 kb
- 2 other attC sites separated by less than 4kb but on the other strand (+)
- 1 other attC site , also on strand +, but separated by more than 4kb.
"""
attc_file = self.find_data(
os.path.join(
"Results_Integron_Finder_{}".format(self.replicon_name),
"tmp_{}".format(self.replicon_id),
"{}_attc_table.res".format(self.replicon_id)))
# Construct attC dataframe (read from infernal file)
attc_df = infernal.read_infernal(attc_file, self.replicon_id,
self.length_cm)
# Add another attC at more than 4kb, same strand
attc_df = attc_df.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 15800,
"pos_end": 16000,
"sens": "+",
"evalue": 1e-3
},
ignore_index=True)
attc_df = attc_df.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 12000,
"pos_end": 12500,
"sens": "+",
"evalue": 1e-3
},
ignore_index=True)
attc_df = attc_df.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 7100,
"pos_end": 8200,
"sens": "+",
"evalue": 1e-3
},
ignore_index=True)
attc_df.sort_values(["Accession_number", "pos_beg", "evalue"],
inplace=True)
# search attC arrays, keeping palindromes
# 2 attc sites are in the same array if they are on the same strand, and separated by
# a distance less than 4kb
attc_array = attc.search_attc(attc_df, True, self.dist_threshold,
self.replicon_size)
self.assertEqual(len(attc_array), 3)
# Construct expected outputs:
attc_res = pd.DataFrame(columns=[
"Accession_number", "cm_attC", "cm_debut", "cm_fin", "pos_beg",
"pos_end", "sens", "evalue"
])
attc_res = attc_res.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 17825,
"pos_end": 17884,
"sens": "-",
"evalue": 1e-9
},
ignore_index=True)
attc_res = attc_res.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 19080,
"pos_end": 19149,
"sens": "-",
"evalue": 1e-4
},
ignore_index=True)
attc_res = attc_res.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 19618,
"pos_end": 19726,
"sens": "-",
"evalue": 1.1e-7
},
ignore_index=True)
attc_res2 = pd.DataFrame(columns=[
"Accession_number", "cm_attC", "cm_debut", "cm_fin", "pos_beg",
"pos_end", "sens", "evalue"
])
attc_res2 = attc_res2.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 12000,
"pos_end": 12500,
"sens": "+",
"evalue": 1e-03
},
ignore_index=True)
attc_res2 = attc_res2.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 15800,
"pos_end": 16000,
"sens": "+",
"evalue": 1e-03
},
ignore_index=True)
attc_res3 = pd.DataFrame(columns=[
"Accession_number", "cm_attC", "cm_debut", "cm_fin", "pos_beg",
"pos_end", "sens", "evalue"
])
attc_res3 = attc_res3.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 7100,
"pos_end": 8200,
"sens": "+",
"evalue": 1e-03
},
ignore_index=True)
# convert positions to int
intcols = ["cm_debut", "cm_fin", "pos_beg", "pos_end"]
attc_res[intcols] = attc_res[intcols].astype(int)
attc_res2[intcols] = attc_res2[intcols].astype(int)
attc_res3[intcols] = attc_res3[intcols].astype(int)
pdt.assert_frame_equal(attc_res, attc_array[2])
pdt.assert_frame_equal(attc_res2, attc_array[1])
pdt.assert_frame_equal(attc_res3, attc_array[0])
def test_find_integron_attC_is_df(self):
replicon_name = 'acba.007.p01.13'
replicon_id = 'ACBA.007.P01_13'
replicon_path = self.find_data(
os.path.join('Replicons', replicon_name + '.fst'))
prot_file = self.find_data(
os.path.join('Proteins', replicon_id + '.prt'))
topologies = Topology('lin')
with FastaIterator(replicon_path) as sequences_db:
sequences_db.topologies = topologies
replicon = next(sequences_db)
attc_file = self.find_data(
os.path.join('Results_Integron_Finder_{}'.format(replicon_name),
'tmp_{}'.format(replicon.id),
'{}_attc_table.res'.format(replicon.id)))
intI_file = self.find_data(
os.path.join('Results_Integron_Finder_{}'.format(replicon_name),
'tmp_{}'.format(replicon.id),
'{}_intI.res'.format(replicon.id)))
phageI_file = self.find_data(
os.path.join('Results_Integron_Finder_{}'.format(replicon_name),
'tmp_{}'.format(replicon.id),
'{}_phage_int.res'.format(replicon.id)))
args = argparse.Namespace()
args.no_proteins = True
args.keep_palindromes = True
args.attc_model = 'attc_4.cm'
args.evalue_attc = 1.0
args.max_attc_size = 200
args.min_attc_size = 40
args.distance_threshold = 4000
args.calin_threshold = 2
args.local_max = False
cfg = Config(args)
cfg._prefix_data = os.path.join(os.path.dirname(__file__), 'data')
len_model_attc = 47 # length in 'CLEN' (value for model attc_4.cm)
attc_file = read_infernal(attc_file,
replicon_name,
len_model_attc,
evalue=cfg.evalue_attc,
size_max_attc=cfg.max_attc_size,
size_min_attc=cfg.min_attc_size)
prot_db = ProdigalDB(replicon, cfg, prot_file=prot_file)
exp_msg = """In replicon {}, there are:
- 0 complete integron(s) found with a total 0 attC site(s)
- 1 CALIN element(s) found with a total of 3 attC site(s)
- 0 In0 element(s) found with a total of 0 attC site""".format(replicon.id)
with self.catch_log() as log:
integrons = find_integron(replicon, prot_db, attc_file, intI_file,
phageI_file, cfg)
catch_msg = log.get_value().strip()
self.assertEqual(catch_msg, exp_msg)
self.assertEqual(len(integrons), 1)
integron = integrons[0]
self.assertEqual(integron.replicon.name, replicon_id)
exp = pd.DataFrame(
{
'annotation': ['attC'] * 3,
'distance_2attC': [np.nan, 1196.0, 469.0],
'evalue': [1.000000e-09, 1.000000e-04, 1.100000e-07],
'model': ['attc_4'] * 3,
'pos_beg': [17825, 19080, 19618],
'pos_end': [17884, 19149, 19726],
'strand': [-1, -1, -1],
'type_elt': 'attC'
},
columns=self.columns,
index=['attc_001', 'attc_002', 'attc_003'])
pdt.assert_frame_equal(integron.attC, exp)
exp = pd.DataFrame(columns=self.columns)
exp = exp.astype(dtype=self.dtype)
pdt.assert_frame_equal(integron.integrase, exp)
pdt.assert_frame_equal(integron.promoter, exp)
pdt.assert_frame_equal(integron.attI, exp)
pdt.assert_frame_equal(integron.proteins, exp)
def test_find_integron_attC_is_df(self):
replicon_name = 'acba.007.p01.13'
replicon_id = 'ACBA.007.P01_13'
replicon_path = self.find_data(os.path.join('Replicons', replicon_name + '.fst'))
prot_file = self.find_data(os.path.join('Proteins', replicon_id + '.prt'))
topologies = Topology('lin')
with FastaIterator(replicon_path) as sequences_db:
sequences_db.topologies = topologies
replicon = next(sequences_db)
attc_file = self.find_data(os.path.join('Results_Integron_Finder_{}'.format(replicon_name),
'tmp_{}'.format(replicon.id),
'{}_attc_table.res'.format(replicon.id)))
intI_file = self.find_data(os.path.join('Results_Integron_Finder_{}'.format(replicon_name),
'tmp_{}'.format(replicon.id),
'{}_intI.res'.format(replicon.id)))
phageI_file = self.find_data(os.path.join('Results_Integron_Finder_{}'.format(replicon_name),
'tmp_{}'.format(replicon.id),
'{}_phage_int.res'.format(replicon.id)))
args = argparse.Namespace()
args.no_proteins = True
args.keep_palindromes = True
args.attc_model = 'attc_4.cm'
args.evalue_attc = 1.0
args.max_attc_size = 200
args.min_attc_size = 40
args.distance_threshold = 4000
args.calin_threshold = 2
args.local_max = False
cfg = Config(args)
cfg._prefix_data = os.path.join(os.path.dirname(__file__), 'data')
len_model_attc = 47 # length in 'CLEN' (value for model attc_4.cm)
attc_file = read_infernal(attc_file, replicon_name,
len_model_attc,
evalue=cfg.evalue_attc,
size_max_attc=cfg.max_attc_size,
size_min_attc=cfg.min_attc_size)
prot_db = ProdigalDB(replicon, cfg, prot_file=prot_file)
exp_msg = """In replicon {}, there are:
- 0 complete integron(s) found with a total 0 attC site(s)
- 1 CALIN element(s) found with a total of 3 attC site(s)
- 0 In0 element(s) found with a total of 0 attC site""".format(replicon.id)
with self.catch_log() as log:
integrons = find_integron(replicon,
prot_db,
attc_file,
intI_file,
phageI_file,
cfg)
catch_msg = log.get_value().strip()
self.assertEqual(catch_msg, exp_msg)
self.assertEqual(len(integrons), 1)
integron = integrons[0]
self.assertEqual(integron.replicon.name, replicon_id)
exp = pd.DataFrame({'annotation': ['attC'] * 3,
'distance_2attC': [np.nan, 1196.0, 469.0],
'evalue': [1.000000e-09, 1.000000e-04, 1.100000e-07],
'model': ['attc_4'] * 3,
'pos_beg': [17825, 19080, 19618],
'pos_end': [17884, 19149, 19726],
'strand': [-1, -1, -1],
'type_elt': 'attC'},
columns=self.columns,
index=['attc_001', 'attc_002', 'attc_003'])
pdt.assert_frame_equal(integron.attC, exp)
exp = pd.DataFrame(columns=self.columns)
exp = exp.astype(dtype=self.dtype)
pdt.assert_frame_equal(integron.integrase, exp)
pdt.assert_frame_equal(integron.promoter, exp)
pdt.assert_frame_equal(integron.attI, exp)
pdt.assert_frame_equal(integron.proteins, exp)
