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_search_attc_drop_pal_break(self):
"""
If there is 1 palindrome attC, check that it keeps the one with the highest evalue,
and that clusters are then found according to it.
"""
attc_df = pd.DataFrame(columns=[
"Accession_number", "cm_attC", "cm_debut", "cm_fin", "pos_beg",
"pos_end", "sens", "evalue"
],
dtype='int')
attc_df = attc_df.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 1000,
"pos_end": 2000,
"sens": "-",
"evalue": 1e-9
},
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": 3000,
"pos_end": 4000,
"sens": "-",
"evalue": 1e-4
},
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": 3000,
"pos_end": 4000,
"sens": "+",
"evalue": 1e-9
},
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": 5500,
"pos_end": 7000,
"sens": "-",
"evalue": 1.1e-7
},
ignore_index=True)
intcols = ["cm_debut", "cm_fin", "pos_beg", "pos_end"]
attc_df[intcols] = attc_df[intcols].astype(int)
attc_array = attc.search_attc(attc_df, False, self.dist_threshold,
self.replicon_size)
self.assertEqual(len(attc_array), 3)
# Construct expected outputs:
columns = [
"Accession_number", "cm_attC", "cm_debut", "cm_fin", "pos_beg",
"pos_end", "sens", "evalue"
]
attc_res = pd.DataFrame(data={
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 1000,
"pos_end": 2000,
"sens": "-",
"evalue": 1e-9
},
index=[0])
attc_res = attc_res[columns]
attc_res2 = pd.DataFrame(data={
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 3000,
"pos_end": 4000,
"sens": "+",
"evalue": 1e-9
},
index=[0])
attc_res2 = attc_res2[columns]
attc_res3 = pd.DataFrame(data={
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 5500,
"pos_end": 7000,
"sens": "-",
"evalue": 1.1e-7
},
index=[0])
attc_res3 = attc_res3[columns]
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_res2, attc_array[0])
pdt.assert_frame_equal(attc_res, attc_array[1])
pdt.assert_frame_equal(attc_res3, attc_array[2])
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_uniq_circ_plus(self):
"""
Test that it finds a unique attc array when giving a table with:
- 2 attC sites at the begining of the genome, separated by less than 4kb
- 2 attC sites at the end of the genome, separated by less than 4kb from the
1st attC site of the genome if we take into account its circularity.
All 3 attC sites are on the same strand +
"""
attc_df = pd.DataFrame(columns=[
"Accession_number", "cm_attC", "cm_debut", "cm_fin", "pos_beg",
"pos_end", "sens", "evalue"
],
dtype='int')
attc_df = attc_df.append(
{
"Accession_number": self.replicon_id,
"cm_attC": "attC_4",
"cm_debut": 1,
"cm_fin": 47,
"pos_beg": 1000,
"pos_end": 2000,
"sens": "+",
"evalue": 1e-9
},
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": 3000,
"pos_end": 4000,
"sens": "+",
"evalue": 1e-4
},
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": 16000,
"pos_end": 17000,
"sens": "+",
"evalue": 1.1e-7
},
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": 19815,
"pos_end": 20000,
"sens": "+",
"evalue": 1.1e-7
},
ignore_index=True)
intcols = ["cm_debut", "cm_fin", "pos_beg", "pos_end"]
attc_df[intcols] = attc_df[intcols].astype(int)
attc_array = attc.search_attc(attc_df, True, self.dist_threshold,
self.replicon_size)
self.assertEqual(len(attc_array), 1)
# Output of search_attc is ordered as the cluster is:
# - 2 last attC of genome
# - 2 first attC of genomes
# Whereas input was ordered by begin position. Reorder attc_df to compare with output.
attc_df = attc_df.reindex([2, 3, 0, 1])
attc_df.reset_index(inplace=True, drop=True)
pdt.assert_frame_equal(attc_df, 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])