def test_fold_rna(self):
"""RNA folding to find min energy secondary structure."""
# unafold's estimates for free energy estimates of RNA oligos
# most tests available at https://github.com/jaswindersingh2/SPOT-RNA/blob/master/sample_inputs/batch_seq.fasta
unafold_dgs = {
"ACCCCCUCCUUCCUUGGAUCAAGGGGCUCAA":
-9.5,
"AAGGGGUUGGUCGCCUCGACUAAGCGGCUUGGAAUUCC":
-10.1,
"UUGGAGUACACAACCUGUACACUCUUUC":
-4.3,
"AGGGAAAAUCCC":
-3.3,
"GCUUACGAGCAAGUUAAGCAAC":
-4.6,
"UGGGAGGUCGUCUAACGGUAGGACGGCGGACUCUGGAUCCGCUGGUGGAGGUUCGAGUCCUCCCCUCCCAGCCA":
-32.8,
"GGGCGAUGAGGCCCGCCCAAACUGCCCUGAAAAGGGCUGAUGGCCUCUACUG":
-20.7,
"GGGGGCAUAGCUCAGCUGGGAGAGCGCCUGCUUUGCACGCAGGAGGUCUGCGGUUCGAUCCCGCGCGCUCCCACCA":
-31.4,
}
for seq, ufold in unafold_dgs.items():
d = dg(seq, temp=37.0)
# accepting a 5% difference
delta = abs(0.5 * min(d, ufold))
self.assertAlmostEqual(d, ufold, delta=delta)
def test_fold_dna(self):
"""DNA folding to find min energy secondary structure."""
# unafold's estimates for free energy estimates of DNA oligos
unafold_dgs = {
"GGGAGGTCGTTACATCTGGGTAACACCGGTACTGATCCGGTGACCTCCC":
-10.94, # three branched structure
"GGGAGGTCGCTCCAGCTGGGAGGAGCGTTGGGGGTATATACCCCCAACACCGGTACTGATCCGGTGACCTCCC":
-23.4, # four branched structure
"CGCAGGGAUACCCGCG":
-3.8,
"TAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGT":
-6.85,
"GGGGGCATAGCTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCTGCGGTTCGATCCCGCGCGCTCCCACCA":
-15.50,
"TGAGACGGAAGGGGATGATTGTCCCCTTCCGTCTCA":
-18.10,
"ACCCCCTCCTTCCTTGGATCAAGGGGCTCAA":
-3.65,
}
for seq, ufold in unafold_dgs.items():
d = dg(seq, temp=37.0)
# accepting a 60% difference
delta = abs(0.6 * min(d, ufold))
self.assertAlmostEqual(d, ufold, delta=delta)
def test_fold_cache(self):
"""Gather a cache of the folded structure."""
seq = "ATGGATTTAGATAGAT"
cache = dg_cache(seq)
seq_dg = dg(seq)
self.assertAlmostEqual(seq_dg, cache[0][len(seq) - 1], delta=1)
def seqfoldScore(queries, returnSS=False):
'''
get the secondary structure for a given sequence
using seqfold here - identical features are available using nupack, though results are sometimes different
:param sequence:
:return:
'''
temperature = 37.0 # celcius
sequences = numbers2letters(queries)
energies = np.zeros(len(sequences))
strings = []
pairLists = []
i = -1
for sequence in sequences:
i += 1
if len(sequence) == 1:
en = np.inf
else:
en = dg(sequence, temp=temperature
) # get predicted minimum energy of folded structure
if np.isfinite(en):
if en > 1500: # no idea why it does this but sometimes it adds 1600 - we will upgrade this to nupack in the future
energies[i] = en - 1600
else:
energies[i] = en
else:
energies[i] = 5 # np.nan # set infinities as being very unlikely
if returnSS:
structs = fold(sequence) # identify structural features
# print(round(sum(s.e for s in structs), 2)) # predicted energy of the final structure
desc = ["."] * len(sequence)
pairList = []
for s in structs:
pairList.append(s.ij[0])
if len(s.ij) == 1:
i, j = s.ij[0]
desc[i] = "("
desc[j] = ")"
ssString = "".join(desc) # secondary structure string
strings.append(ssString)
pairList = np.asarray(pairList) + 1 # list of paired bases
pairLists.append(pairList)
if returnSS:
return energies, strings, pairLists
else:
return energies
def test_fold(self):
"""Fold function."""
# it should throw if a nonsense sequence is provided
with self.assertRaises(RuntimeError):
dg("EASFEASFAST", 37.0)
# Both U and T, mix of RNA and DNA
with self.assertRaises(RuntimeError):
dg("ATGCATGACGATUU", 37.0)
# should not throw
dg("ATGGATTTAGATAGAT")