def test_rnaalifold_output(self):
"""Test for rnaalifold format parser"""
#Test empty lines
self.assertEqual(MinimalRnaalifoldParser(''), [])
#Test one structure
obs = MinimalRnaalifoldParser(self.rnaalifold_out)
self.assertEqual(obs, self.rnaalifold_exp)
#Test two structures
obs_2 = MinimalRnaalifoldParser(self.rnaalifold_out_2)
self.assertEqual(obs_2, self.rnaalifold_exp_2)
def get_constrained_fold(sequence, constraint_string, params=None):
"""Returns secondary structure from RNAfold with constraints.
- sequence: RNA sequence object or string.
- constraint_string: RNAfold folding constraint string.
- params: dict of additional RNAfold parameters.
"""
#Check that sequence and constraint string exist.
if not sequence:
raise ValueError, 'No sequence found!'
elif not constraint_string:
raise ValueError, 'No constraint string found!'
sequence = str(sequence)
#Check that sequence and constraint_string are equal length.
if len(sequence) != len(constraint_string):
raise ValueError, 'Sequence and constraint string are not same length!'
app = RNAfold(params=params)
#Turn on constrained folding.
app.Parameters['-C'].on()
res = app([sequence,constraint_string])
#Parse out seq, struct string and energy.
seq, struct, energy = MinimalRnaalifoldParser(res['StdOut'].readlines())[0]
#Clean up after application.
res.cleanUp()
return seq, struct, energy
def rnaalifold_from_alignment(aln, moltype=RNA, params=None):
"""Returns seq, pairs, folding energy for alignment.
"""
#Create Alignment object. Object will handle if seqs are unaligned.
aln = Alignment(aln, MolType=RNA)
int_map, int_keys = aln.getIntMap()
app = RNAalifold(WorkingDir='/tmp',\
InputHandler='_input_as_multiline_string',params=params)
res = app(clustal_from_alignment(int_map))
#seq,pairs,energy = rnaalifold_parser(res['StdOut'].readlines())
pairs_list = MinimalRnaalifoldParser(res['StdOut'].readlines())
res.cleanUp()
return pairs_list
def get_secondary_structure(sequence, params=None):
"""Returns secondary structure from RNAfold.
- sequence: RNA sequence object or string.
- params: dict of additional RNAfold parameters.
"""
#Check that sequence and constraint string exist.
if not sequence:
raise ValueError, 'No sequence found!'
sequence = str(sequence)
app = RNAfold(params=params)
res = app([sequence])
#Parse out seq, struct string and energy.
seq, struct, energy = MinimalRnaalifoldParser(res['StdOut'].readlines())[0]
#Clean up after application.
res.cleanUp()
return seq, struct, energy