def _parse(self):
tmp_ct = []
defline = ">"
for line in open(self.ct_path):
if line.startswith('#'):
defline += line.strip() + '|'
else:
tmp_ct.append(line)
defline = defline.replace('\n', '').replace('#', '')
# just one entry per file
result = ct_parser(tmp_ct)[0]
sequence = result[0]
# IMPORTANT!
# ct_parser starts numbering of base pairs from 0, not from 1, as
# elsewhere in nucleic.secstruc. To make things consistent, here
# we'll add 1 to each index in base pairs list!
result_1 = [(pair[0] + 1, pair[1] + 1) for pair in result[1]]
pairs = BasePairs(result_1)
if self._is_valid_sequence(sequence):
sequence = Sequence(sequence.upper()).seq_without_modifications
# Second check, because ModeRNA might also mix a bit at this stage
# including for exampel X in sequences without modifications!
if self._is_valid_sequence(sequence):
try:
vienna = pairs.toVienna(len(sequence))
except PseudoknotTokensError:
vienna = None
finally:
return defline, sequence, vienna, pairs
return None, None, None, None
def carnac_parser(lines=None):
"""Parser for carnac output
tested in test_ct"""
result = ct_parser(lines)
return result
def carnac_parser(lines=None):
"""Parser for carnac output
tested in test_ct"""
result = ct_parser(lines)
return result
def knetfold_parser(lines):
"""Parser for knetfold output"""
result = ct_parser(lines)
return result
def test_knetfold_output(self):
"""Test for ct_parser for knetfold format"""
obs = ct_parser(self.knetfold_out)
self.assertEqual(obs, self.knetfold_exp)
def test_dynalign_output(self):
"""Test for ct_parser for dynalign format"""
obs = ct_parser(self.dynalign_out)
self.assertEqual(obs, self.dynalign_exp)
def test_carnac_output(self):
"""Test for ct_parser for carnac format"""
obs = ct_parser(self.carnac_out)
self.assertEqual(obs, self.carnac_exp)
def unafold_parser(lines=None):
"""Parser for unafold output"""
result = ct_parser(lines)
return result
def sfold_parser(lines):
"""Parser for Sfold output"""
result = ct_parser(lines)
return result
def test_knetfold_output(self):
"""Test for ct_parser for knetfold format"""
obs = ct_parser(self.knetfold_out)
self.assertEqual(obs,self.knetfold_exp)
def test_dynalign_output(self):
"""Test for ct_parser for dynalign format"""
obs = ct_parser(self.dynalign_out)
self.assertEqual(obs,self.dynalign_exp)
def test_carnac_output(self):
"""Test for ct_parser for carnac format"""
obs = ct_parser(self.carnac_out)
self.assertEqual(obs,self.carnac_exp)
def knetfold_parser(lines):
"""Parser for knetfold output"""
result = ct_parser(lines)
return result
def mfold_parser(lines=None):
"""Parser for Mfold output"""
result = ct_parser(lines)
return result
def dynalign_parser(lines=None):
"""Parser for dynalign output"""
result = ct_parser(lines)
return result
def dynalign_parser(lines=None):
"""Parser for dynalign output"""
result = ct_parser(lines)
return result
