def local_max_end_beg(self):
win_beg = 942899
win_end = 947099
strand_search = 'top'
local_max_received = infernal.local_max(
self.replicon,
win_beg,
win_end,
self.model_attc_path,
strand_search=strand_search,
evalue_attc=self.evalue_attc,
max_attc_size=self.max_attc_size,
min_attc_size=self.min_attc_size,
cmsearch_bin=self.cmsearch,
out_dir=self.out_dir,
cpu_nb=self.cpu_nb)
local_max_expected = pd.DataFrame([[
'LIAN.001.C02_10', 'attC_4', 1, 47, 943270, 943395, '+', 0.13
], [
'LIAN.001.C02_10', 'attC_4', 1, 47, 944008, 944133, '+', 0.049
], ['LIAN.001.C02_10', 'attC_4', 1, 47, 944472, 944598, '+', 4.7e-06]],
columns=[
'Accession_number', 'cm_attC',
'cm_debut', 'cm_fin', 'pos_beg',
'pos_end', 'sens', 'evalue'
])
pdt.assert_frame_equal(local_max_expected, local_max_received)
def test_local_max_cmsearch_bad_rc(self):
win_beg = 942899
win_end = 947099
strand_search = 'top'
infernal.call = lambda x, stdout=None: 1
with self.assertRaises(RuntimeError) as ctx:
_ = infernal.local_max(self.replicon,
win_beg, win_end,
self.model_attc_path,
strand_search=strand_search,
evalue_attc=self.evalue_attc,
max_attc_size=self.max_attc_size, min_attc_size=self.min_attc_size,
out_dir=self.out_dir, cpu_nb=self.cpu_nb
)
self.assertTrue(str(ctx.exception).endswith("failed returncode = {}".format(infernal.call(None))))
def test_no_local_max_bottom(self):
win_beg = 930689
win_end = 934889
strand_search = 'bottom'
local_max_received = infernal.local_max(self.replicon,
win_beg, win_end,
self.model_attc_path,
strand_search=strand_search,
evalue_attc=self.evalue_attc,
max_attc_size=self.max_attc_size, min_attc_size=self.min_attc_size,
cmsearch_bin=self.cmsearch, out_dir=self.out_dir, cpu_nb=self.cpu_nb
)
local_max_expected = pd.DataFrame(columns=['Accession_number', 'cm_attC', 'cm_debut', 'cm_fin', 'pos_beg',
'pos_end', 'sens', 'evalue'])
pdt.assert_frame_equal(local_max_expected, local_max_received)
def test_local_max_cmsearch_failed(self):
win_beg = 942899
win_end = 947099
strand_search = 'top'
cmsearch_bin = 'failed_cmsearch'
with self.assertRaises(RuntimeError) as ctx:
_ = infernal.local_max(self.replicon,
win_beg, win_end,
self.model_attc_path,
strand_search=strand_search,
evalue_attc=self.evalue_attc,
max_attc_size=self.max_attc_size, min_attc_size=self.min_attc_size,
cmsearch_bin=cmsearch_bin, out_dir=self.out_dir, cpu_nb=self.cpu_nb
)
self.assertTrue(re.search("failed : \[Errno 2\] No such file or directory: '{}'".format(cmsearch_bin),
str(ctx.exception)))
def local_max_end_beg(self):
win_beg = 942899
win_end = 947099
strand_search = 'top'
local_max_received = infernal.local_max(self.replicon,
win_beg, win_end,
self.model_attc_path,
strand_search=strand_search,
evalue_attc=self.evalue_attc,
max_attc_size=self.max_attc_size, min_attc_size=self.min_attc_size,
cmsearch_bin=self.cmsearch, out_dir=self.out_dir, cpu_nb=self.cpu_nb
)
local_max_expected = pd.DataFrame([['LIAN.001.C02_10', 'attC_4', 1, 47, 943270, 943395, '+', 0.13],
['LIAN.001.C02_10', 'attC_4', 1, 47, 944008, 944133, '+', 0.049],
['LIAN.001.C02_10', 'attC_4', 1, 47, 944472, 944598, '+', 4.7e-06]],
columns=['Accession_number', 'cm_attC', 'cm_debut', 'cm_fin', 'pos_beg',
'pos_end', 'sens', 'evalue'])
pdt.assert_frame_equal(local_max_expected, local_max_received)
def test_local_max_cmsearch_bad_rc(self):
win_beg = 942899
win_end = 947099
strand_search = 'top'
infernal.call = lambda x, stdout=None: 1
with self.assertRaises(RuntimeError) as ctx:
_ = infernal.local_max(self.replicon,
win_beg,
win_end,
self.model_attc_path,
strand_search=strand_search,
evalue_attc=self.evalue_attc,
max_attc_size=self.max_attc_size,
min_attc_size=self.min_attc_size,
out_dir=self.out_dir,
cpu_nb=self.cpu_nb)
self.assertTrue(
str(ctx.exception).endswith("failed returncode = {}".format(
infernal.call(None))))
def test_no_local_max_bottom(self):
win_beg = 930689
win_end = 934889
strand_search = 'bottom'
local_max_received = infernal.local_max(
self.replicon,
win_beg,
win_end,
self.model_attc_path,
strand_search=strand_search,
evalue_attc=self.evalue_attc,
max_attc_size=self.max_attc_size,
min_attc_size=self.min_attc_size,
cmsearch_bin=self.cmsearch,
out_dir=self.out_dir,
cpu_nb=self.cpu_nb)
local_max_expected = pd.DataFrame(columns=[
'Accession_number', 'cm_attC', 'cm_debut', 'cm_fin', 'pos_beg',
'pos_end', 'sens', 'evalue'
])
pdt.assert_frame_equal(local_max_expected, local_max_received)
def test_local_max_cmsearch_failed(self):
win_beg = 942899
win_end = 947099
strand_search = 'top'
cmsearch_bin = 'failed_cmsearch'
with self.assertRaises(RuntimeError) as ctx:
_ = infernal.local_max(self.replicon,
win_beg,
win_end,
self.model_attc_path,
strand_search=strand_search,
evalue_attc=self.evalue_attc,
max_attc_size=self.max_attc_size,
min_attc_size=self.min_attc_size,
cmsearch_bin=cmsearch_bin,
out_dir=self.out_dir,
cpu_nb=self.cpu_nb)
self.assertTrue(
re.search(
"failed : \[Errno 2\] No such file or directory: '{}'".format(
cmsearch_bin), str(ctx.exception)))
