def format_pairmap(struc):
pm = get_pairmap_from_secstruct(struc)
new = []
for i in pm:
if i == -1:
new.append(i)
else:
i += 1
new.append(i)
return pm
def pairmap_from_sequence(
seq,
vienna_version,
vienna_path='../../../EteRNABot/eternabot/./RNAfold'):
new_struc = ''
if vienna_version == 1:
if sys.version_info[:3] > (3, 0):
p = Popen([vienna_path, '-T', '37.0'],
stdout=PIPE,
stdin=PIPE,
stderr=STDOUT,
encoding='utf8')
else:
p = Popen([vienna_path, '-T', '37.0'],
stdout=PIPE,
stdin=PIPE,
stderr=STDOUT)
pair = p.communicate(input=''.join(seq))[0]
formatted = re.split('\s+| \(?\s?', pair)
new_struc = formatted[1]
elif vienna_version == 2:
new_struc = RNA.fold(''.join(seq))[0]
return get_pairmap_from_secstruct(new_struc)
def dsp(dot_bracket,
seq_str,
vienna_version='1',
vienna_path='../../../EteRNABot/eternabot/./RNAfold'
): # domain specific pipeline
'''
Adds player strategies via a MCTS
:param dot_bracket: The target structure of the RNA in dot-bracket notation
:param seq_str: The current RNA sequence
:param vienna_version: Vienna 1.8.5 or Vienna 2
:param vienna_path: Path to the Vienna 1.8.5 RNAfold
:return: The updated RNA sequence after the DSP
'''
try:
vienna_version = int(vienna_version)
except TypeError:
raise TypeError('Please pass in a valid Vienna version')
assert (vienna_version <= 2, "Please pass in a valid Vienna version")
assert (vienna_version >= 1, "Please pass in a valid Vienna version")
seq = list(seq_str)
m = []
SOLVE = False
current_struc, _ = RNA.fold(seq_str)
target_struc = encode_struc(dot_bracket)
target_pm = get_pairmap_from_secstruct(dot_bracket)
current_pm = get_pairmap_from_secstruct(current_struc)
pairs = find_parens(dot_bracket)
#print target_pm
#print current_pm
"""
Correcting incorrect base pairings
"""
############ Comment out from here to remove this strategy #############
for base1, base2 in pairs.items(): # corrects incorrect base pairings
#print base1,base2
if (seq[base1] == 'A'
and seq[base2] == 'U') or (seq[base1] == 'U'
and seq[base2] == 'A'):
continue
elif (seq[base1] == 'G'
and seq[base2] == 'U') or (seq[base1] == 'U'
and seq[base2] == 'G'):
continue
elif (seq[base1] == 'G'
and seq[base2] == 'C') or (seq[base1] == 'C'
and seq[base2] == 'G'):
continue
elif (seq[base1] == 'G' and seq[base2] == 'A'):
seq[base1] = 'U'
m.append([2, base1 + 1])
elif (seq[base1] == 'A' and seq[base2] == 'G'):
seq[base1] = 'C'
m.append([4, base1 + 1])
elif (seq[base1] == 'C' and seq[base2] == 'U'):
seq[base1] = 'A'
m.append([1, base1 + 1])
elif (seq[base1] == 'U' and seq[base2] == 'C'):
seq[base1] = 'G'
m.append([3, base1 + 1])
elif (seq[base1] == 'A' and seq[base2] == 'C'):
seq[base1] = 'G'
m.append([3, base1 + 1])
elif (seq[base1] == 'C' and seq[base2] == 'A'):
seq[base1] = 'U'
m.append([2, base1 + 1])
elif (seq[base1] == 'A' and seq[base2] == 'A'):
seq[base1] = 'U'
m.append([2, base1 + 1])
elif (seq[base1] == 'U' and seq[base2] == 'U'):
seq[base1] = 'A'
m.append([1, base1 + 1])
elif (seq[base1] == 'G' and seq[base2] == 'G'):
seq[base1] = 'C'
m.append([4, base1 + 1])
elif (seq[base1] == 'C' and seq[base2] == 'C'):
seq[base1] = 'G'
m.append([3, base1 + 1])
#print ''.join(seq)
for i in range(len(target_pm)):
if target_pm[i] == -1:
seq[i] = 'A'
m.append([1, i + 1])
else:
continue
######################################################################
"""
End pairs to G-C
"""
############ Comment out from here to remove this strategy #############
for i in range(len(dot_bracket)):
try:
if dot_bracket[i] == '(': # or dot_bracket[i] == ')':
#print dot_bracket[i]
if dot_bracket[i - 1] == '.' or dot_bracket[
i - 1] == ')' or dot_bracket[
i + 1] == '.' or dot_bracket[i + 1] == ')':
#print i
if (seq[i] == 'G' and seq[target_pm[i]] == 'C') or (
seq[i] == 'C' and seq[target_pm[i]] == 'G'):
continue
else:
seq[i] = 'G'
seq[target_pm[i]] = 'C'
m.append([3, i + 1])
m.append([4, target_pm[i] + 1])
# elif dot_bracket[i+1] == '.' and dot_bracket[i+2] == '.' and dot_bracket[i+3] == '.' and dot_bracket[i+4] == '.':
# seq[i+1] = 'G'
elif dot_bracket[i] == ')': # or dot_bracket[i] == ')':
#print dot_bracket[i]
if dot_bracket[i - 1] == '.' or dot_bracket[
i - 1] == '(' or dot_bracket[
i + 1] == '.' or dot_bracket[i + 1] == '(':
#print i
if (seq[i] == 'G' and seq[target_pm[i]] == 'C') or (
seq[i] == 'C' and seq[target_pm[i]] == 'G'):
continue
else:
seq[i] = 'G'
seq[target_pm[i]] = 'C'
m.append([3, i + 1])
m.append([4, target_pm[i] + 1])
except IndexError:
continue
######################################################################
"""
G External Loop Boost
"""
############ Comment out from here to remove this strategy #############
for i in range(len(dot_bracket)):
if dot_bracket[i] == '(':
if dot_bracket[i + 1] == '.' and dot_bracket[
i + 2] == '.' and dot_bracket[
i + 3] == '.' and dot_bracket[i + 4] == '.':
seq[i + 1] = 'G'
m.append([3, i + 2])
# elif (dot_bracket[i+1] == '.' and dot_bracket[i+2] == '('):
# seq[i+1] = 'G'
########################################################################
"""
G-A Internal Loop Boost
"""
############ Comment out ######################################################
for i in range(len(dot_bracket)):
#pairing = target_pm[i]
if dot_bracket[i] == '(' and dot_bracket[
i +
1] == '.': # and dot_bracket[target_pm[i]] == ")" and dot_bracket[target_pm[i-1]] == '.':
leftdots = []
starter = 0
for j in range(i + 1, len(dot_bracket)):
if dot_bracket[j] == '(': # or dot_bracket[j] == ')':
starter = j
break
leftdots.append(dot_bracket[j])
rightdots = []
idx = target_pm[i]
ender = 0
for k in range(idx - 1, -1, -1):
if dot_bracket[k] == ')': # or dot_bracket[k] == '(':
ender = k
break
rightdots.append(dot_bracket[k])
if len(leftdots) > 0 and len(rightdots) > 0:
if (len(leftdots) != 2 or len(rightdots) != 2) and (
math.fabs(len(rightdots) - len(leftdots)) <= 5):
if target_pm[starter] == starter or target_pm[
starter] == ender:
seq[i + 1] = 'G'
seq[ender + 1] = 'G'
##############################################################################
# if dot_bracket[i] == ')' and dot_bracket[i+1] == '.' and dot_bracket[target_pm[i]] == "(" and dot_bracket[target_pm[i+1]] == '.':
# dots = []
# starter = 0
# for j in range(i+1, len(dot_bracket)):
# if dot_bracket[j] == ')':
# starter = j
# break
# dots.append(dot_bracket[j])
#
# idx = target_pm[i]
# ender = 0
# for k in range(idx-1,-1,-1):
# if dot_bracket[k] == '(':
# ender = k
# break
# dots.append(dot_bracket[k])
#
# if dots.count(dots[0]) == len(dots) and target_pm[ender] == starter:
# seq[i+1] = 'G'
# seq[ender+1] = 'G'
"""
U-G-U-G Superboost
"""
############ Comment out from here to remove this strategy #############
if dot_bracket[i] == '(' and dot_bracket[i + 1] == '.' and dot_bracket[
i + 2] == '.' and dot_bracket[i + 3] == '(': # UGUG superboost
idx = target_pm[i]
dots = []
starter = 0
for j in range(i + 1, len(dot_bracket)):
if dot_bracket[j] == '(':
starter = j
break
dots.append(dot_bracket[j])
idx = target_pm[i]
ender = 0
for k in range(idx - 1, -1, -1):
if dot_bracket[k] == ')':
ender = k
break
dots.append(dot_bracket[k])
if dot_bracket[idx] == ')' and dot_bracket[
idx -
1] == '.' and dot_bracket[idx - 2] == '.' and dot_bracket[
idx - 3] == ')' and target_pm[ender] == starter:
seq[i + 1] = 'U'
seq[i + 2] = 'G'
seq[idx - 2] = 'U'
seq[idx - 1] = 'G'
m.append([2, i + 2])
m.append([3, i + 3])
m.append([2, idx - 1])
m.append([3, idx])
elif dot_bracket[idx] == ')' and dot_bracket[
idx - 1] == '.' and dot_bracket[idx - 2] == ')':
seq[i + 1] = 'G'
seq[idx - 1] = 'G'
m.append([3, i + 2])
m.append([3, idx])
######################################################################
# if dot_bracket[i] == '(' and dot_bracket[i+1] == '.' and dot_bracket[i+2] == '(': # G-G in 2 pair internal loop
# idx = target_pm[i]
# if dot_bracket[idx] == ')' and dot_bracket[idx-1] == '.' and dot_bracket[idx-2] == ')':
# seq[i+1] = 'G'
# seq[idx-1] = 'G'
# m.append([3,i+2])
# m.append([3,idx])
# elif dot_bracket[idx] == ')' and dot_bracket[idx-1] == '.' and dot_bracket[idx-2] == '.' and dot_bracket[idx-3] == ')':
# seq[i+1] = 'G'
# seq[idx-1] = 'G'
# m.append([3,i+2])
# m.append([3,idx])
#
# if dot_bracket[i] == '(' and dot_bracket[i+1] == '.' and dot_bracket[i+2] == '.' and dot_bracket[i+3] == '.' and dot_bracket[i+4] == '(': # G-G in 2 pair internal loop
# idx = target_pm[i]
# if dot_bracket[idx] == ')' and dot_bracket[idx-1] == '.' and dot_bracket[idx-2] == '.' and dot_bracket[idx-3] == '.' and dot_bracket[idx-4] == ')':
# seq[i+1] = 'G'
# seq[idx-3] = 'G'
# m.append([3,i+2])
# m.append([3,idx])
# elif dot_bracket[idx] == ')' and dot_bracket[idx-1] == '.' and dot_bracket[idx-2] == '.' and dot_bracket[idx-3] == ')':
# seq[i+1] = 'G'
# seq[idx-1] = 'G'
# m.append([3,i+2])
# m.append([3,idx])
'''
Flips base pairs
'''
############ Comment out from here to remove this strategy #############
new_pm = pairmap_from_sequence(seq, vienna_version)
match = SequenceMatcher(None, new_pm, target_pm).ratio()
for j in range(5):
for i in range(len(dot_bracket)):
if new_pm == target_pm:
print('puzzle solved')
SOLVE = True
break
else:
if new_pm[i] == target_pm[i]:
continue
else:
paired = target_pm[i]
base1 = seq[i]
base2 = seq[paired]
if paired == -1: continue
seq[i] = base2
seq[paired] = base1
new_pm = pairmap_from_sequence(seq, vienna_version)
new_match = SequenceMatcher(None, new_pm,
target_pm).ratio()
if new_match > match:
match = copy.deepcopy(new_match)
m.append([str_to_num(seq[i]), i + 1])
m.append([str_to_num(seq[paired]), paired + 1])
else:
seq[i] = base1
seq[paired] = base2
######################################################################
for i in range(len(dot_bracket)):
if new_pm[i] == target_pm[i]:
continue
else:
paired = target_pm[i]
seq[i] = 'G'
seq[paired] = 'C'
m.append([3, i + 1])
m.append([4, paired + 1])
for j in range(3):
for i in range(len(dot_bracket)):
if new_pm == target_pm:
print('puzzle solved')
SOLVE = True
break
else:
if new_pm[i] == target_pm[i]:
continue
else:
paired = target_pm[i]
base1 = seq[i]
base2 = seq[paired]
if paired == -1: continue
seq[i] = base2
seq[paired] = base1
new_pm = pairmap_from_sequence(seq, vienna_version)
new_match = SequenceMatcher(None, new_pm,
target_pm).ratio()
if new_match > match:
match = copy.deepcopy(new_match)
m.append([str_to_num(seq[i]), i + 1])
m.append([str_to_num(seq[paired]), paired + 1])
else:
seq[i] = base1
seq[paired] = base2
return ''.join(seq), m, SOLVE
cs, _ = RNA.fold(''.join(seq))
current_pm = get_pairmap_from_secstruct(cs)
def sbc(dot_bracket, seq): # Monte Carlo Tree Search with Depth 1
'''
Mutates individual bases with MCTS
:param dot_bracket: The target structure for the RNA in dot-bracket notation
:param seq: The current RNA sequence
:return: An updated RNA sequence after the SBC
'''
movesets = []
target_struc = encode_struc(dot_bracket)
pm = get_pairmap_from_secstruct(dot_bracket)
SOLVE = False
#cdb = '.((((....))))'
#current_struc = encode_struc(cdb)
#percent_match = similar(dot_bracket,cdb)
len_puzzle = len(target_struc)
len_puzzle_float = len(target_struc) * 1.0
# GAACGCACCUGCCUGUUUGGGGAGUAUGAA GAACGCACCUGCCUGUUUGGGUAGCAUGAA
# GAACGCACCUGCCUGUCUGGGUAGCAUGAA GAACUCACCUGCCUGUCUUGGUAGCAUCAA
# global current_seq
current_seq = convert_to_list(seq)
cdb, _ = RNA.fold(seq)
current_pm = get_pairmap_from_secstruct(cdb)
for i in range(4):
for location in range(len_puzzle):
if dot_bracket == cdb:
# print current_seq
# print convert_to_str(current_seq)
# print 'Puzzle Solved'
SOLVE = True
break
else:
#percent_match = similar(dot_bracket,cdb)
A = 1
U = 2
G = 3
C = 4
a_change = hot_one_state(current_seq, location, A)
u_change = hot_one_state(current_seq, location, U)
g_change = hot_one_state(current_seq, location, G)
c_change = hot_one_state(current_seq, location, C)
a_struc = get_pairmap_from_secstruct(
convert_to_struc(a_change))
u_struc = get_pairmap_from_secstruct(
convert_to_struc(u_change))
g_struc = get_pairmap_from_secstruct(
convert_to_struc(g_change))
c_struc = get_pairmap_from_secstruct(
convert_to_struc(c_change))
# print '\n'
# # print a_struc
# # print u_struc
# # print g_struc
# # print c_struc
# print dot_bracket
# a_reward = SequenceMatcher(None,a_struc,pm)
# u_reward = SequenceMatcher(None,u_struc,pm)
# g_reward = SequenceMatcher(None,g_struc,pm)
# c_reward = SequenceMatcher(None,c_struc,pm)
a_reward = similar(a_struc, pm)
u_reward = similar(u_struc, pm)
g_reward = similar(g_struc, pm)
c_reward = similar(c_struc, pm)
# a_reward = eternabot_score(a_struc)
# u_reward = eternabot_score(u_struc)
# g_reward = eternabot_score(g_struc)
# c_reward = eternabot_score(c_struc)
# print a_reward,u_reward,g_reward,c_reward
changes = [a_reward, u_reward, g_reward, c_reward]
# total = sum(changes)
# base_array = [x / total for x in changes]
# best_move = (choice([1,2,3,4],1,p=base_array,replace=False))[0]
if all_same(changes) != True:
indices = [
i for i, x in enumerate(changes) if x == max(changes)
]
best_move = choice(indices) + 1
new_seq = hot_one_state(current_seq, location, best_move)
current_seq = new_seq
cdb = convert_to_struc(current_seq)
m = [best_move, location]
movesets.append(m)
else:
pass
# print current_seq
reg = []
# print convert_to_str(current_seq)
# print cdb
current_pm = get_pairmap_from_secstruct(cdb)
# print len(list(set(current_pm) & set(pm)))/float((len(pm)))
return convert_to_str(current_seq), movesets, SOLVE
def dsp(dot_bracket,seq_str): # domain specific pipeline
'''
Adds player strategies via a MCTS
:param dot_bracket: The target structure of the RNA in dot-bracket notation
:param seq_str: The current RNA sequence
:return: The updated RNA sequence after the DSP
'''
seq = list(seq_str)
m = []
SOLVE = False
current_struc,_ = RNA.fold(seq_str)
target_struc = encode_struc(dot_bracket)
target_pm = get_pairmap_from_secstruct(dot_bracket)
current_pm = get_pairmap_from_secstruct(current_struc)
pairs = find_parens(dot_bracket)
#print target_pm
#print current_pm
for base1,base2 in pairs.iteritems(): # corrects incorrect base pairings
#print base1,base2
if (seq[base1] == 'A' and seq[base2] == 'U') or (seq[base1] == 'U' and seq[base2] == 'A'):
continue
elif (seq[base1] == 'G' and seq[base2] == 'U') or (seq[base1] == 'U' and seq[base2] == 'G'):
continue
elif (seq[base1] == 'G' and seq[base2] == 'C') or (seq[base1] == 'C' and seq[base2] == 'G'):
continue
elif (seq[base1] == 'G' and seq[base2] == 'A'):
seq[base1] = 'U'
m.append([2,base1+1])
elif (seq[base1] == 'A' and seq[base2] == 'G'):
seq[base1] = 'C'
m.append([4,base1+1])
elif (seq[base1] == 'C' and seq[base2] == 'U'):
seq[base1] = 'A'
m.append([1,base1+1])
elif (seq[base1] == 'U' and seq[base2] == 'C'):
seq[base1] = 'G'
m.append([3,base1+1])
elif (seq[base1] == 'A' and seq[base2] == 'C'):
seq[base1] = 'G'
m.append([3,base1+1])
elif (seq[base1] == 'C' and seq[base2] == 'A'):
seq[base1] = 'U'
m.append([2,base1+1])
elif (seq[base1] == 'A' and seq[base2] == 'A'):
seq[base1] = 'U'
m.append([2,base1+1])
elif (seq[base1] == 'U' and seq[base2] == 'U'):
seq[base1] = 'A'
m.append([1,base1+1])
elif (seq[base1] == 'G' and seq[base2] == 'G'):
seq[base1] = 'C'
m.append([4,base1+1])
elif (seq[base1] == 'C' and seq[base2] == 'C'):
seq[base1] = 'G'
m.append([3,base1+1])
#print ''.join(seq)
for i in range(len(target_pm)):
if target_pm[i] == -1:
seq[i] = 'A'
m.append([1,i+1])
else:
continue
for i in range(len(dot_bracket)):
try:
if dot_bracket[i] == '(':# or dot_bracket[i] == ')':
#print dot_bracket[i]
if dot_bracket[i-1] == '.' or dot_bracket[i-1] == ')' or dot_bracket[i+1] == '.' or dot_bracket[i+1] == ')':
#print i
if (seq[i] == 'G' and seq[target_pm[i]] == 'C') or (seq[i] == 'C' and seq[target_pm[i]] == 'G'):
continue
else:
seq[i] = 'G'
seq[target_pm[i]] = 'C'
m.append([3,i+1])
m.append([4,target_pm[i]+1])
# elif dot_bracket[i+1] == '.' and dot_bracket[i+2] == '.' and dot_bracket[i+3] == '.' and dot_bracket[i+4] == '.':
# seq[i+1] = 'G'
elif dot_bracket[i] == ')':# or dot_bracket[i] == ')':
#print dot_bracket[i]
if dot_bracket[i-1] == '.' or dot_bracket[i-1] == '(' or dot_bracket[i+1] == '.' or dot_bracket[i+1] == '(':
#print i
if (seq[i] == 'G' and seq[target_pm[i]] == 'C') or (seq[i] == 'C' and seq[target_pm[i]] == 'G'):
continue
else:
seq[i] = 'G'
seq[target_pm[i]] = 'C'
m.append([3,i+1])
m.append([4,target_pm[i]+1])
except IndexError:
continue
for i in range(len(dot_bracket)):
if dot_bracket[i] == '(':
if dot_bracket[i+1] == '.' and dot_bracket[i+2] == '.' and dot_bracket[i+3] == '.' and dot_bracket[i+4] == '.':
seq[i+1] = 'G'
m.append([3,i+2])
# elif (dot_bracket[i+1] == '.' and dot_bracket[i+2] == '('):
# seq[i+1] = 'G'
for i in range(len(dot_bracket)):
if dot_bracket[i] == '(' and dot_bracket[i+1] == '.':
dots = []
starter = 0
for j in range(i+1, len(dot_bracket)):
if dot_bracket[j] == '(':
starter = j
break
dots.append(dot_bracket[j])
idx = target_pm[i]
ender = 0
for k in range(idx-1,-1,-1):
if dot_bracket[k] == ')':
ender = k
break
dots.append(dot_bracket[k])
if dots.count(dots[0]) == len(dots) and target_pm[ender] == starter:
seq[i+1] = 'G'
seq[ender+1] = 'G'
if dot_bracket[i] == '(' and dot_bracket[i+1] == '.' and dot_bracket[i+2] == '.' and dot_bracket[i+3] == '(': # UGUG superboost
idx = target_pm[i]
if dot_bracket[idx] == ')' and dot_bracket[idx-1] == '.' and dot_bracket[idx-2] == '.' and dot_bracket[idx-3] == ')':
seq[i+1] = 'U'
seq[i+2] = 'G'
seq[idx-2] = 'U'
seq[idx-1] = 'G'
m.append([2,i+2])
m.append([3,i+3])
m.append([2,idx-1])
m.append([3,idx])
elif dot_bracket[idx] == ')' and dot_bracket[idx-1] == '.' and dot_bracket[idx-2] == ')':
seq[i+1] = 'G'
seq[idx-1] = 'G'
m.append([3,i+2])
m.append([3,idx])
# if dot_bracket[i] == '(' and dot_bracket[i+1] == '.' and dot_bracket[i+2] == '(': # G-G in 2 pair internal loop
# idx = target_pm[i]
# if dot_bracket[idx] == ')' and dot_bracket[idx-1] == '.' and dot_bracket[idx-2] == ')':
# seq[i+1] = 'G'
# seq[idx-1] = 'G'
# m.append([3,i+2])
# m.append([3,idx])
# elif dot_bracket[idx] == ')' and dot_bracket[idx-1] == '.' and dot_bracket[idx-2] == '.' and dot_bracket[idx-3] == ')':
# seq[i+1] = 'G'
# seq[idx-1] = 'G'
# m.append([3,i+2])
# m.append([3,idx])
#
# if dot_bracket[i] == '(' and dot_bracket[i+1] == '.' and dot_bracket[i+2] == '.' and dot_bracket[i+3] == '.' and dot_bracket[i+4] == '(': # G-G in 2 pair internal loop
# idx = target_pm[i]
# if dot_bracket[idx] == ')' and dot_bracket[idx-1] == '.' and dot_bracket[idx-2] == '.' and dot_bracket[idx-3] == '.' and dot_bracket[idx-4] == ')':
# seq[i+1] = 'G'
# seq[idx-3] = 'G'
# m.append([3,i+2])
# m.append([3,idx])
# elif dot_bracket[idx] == ')' and dot_bracket[idx-1] == '.' and dot_bracket[idx-2] == '.' and dot_bracket[idx-3] == ')':
# seq[i+1] = 'G'
# seq[idx-1] = 'G'
# m.append([3,i+2])
# m.append([3,idx])
'''
Randomly flips base pairs
'''
p = Popen(['../../../EteRNABot/eternabot/./RNAfold', '-T','37.0'], stdout=PIPE, stdin=PIPE, stderr=STDOUT)
pair = p.communicate(input=''.join(seq))[0]
formatted = re.split('\s+| \(?\s?',pair)
new_struc = formatted[1]
new_pm = get_pairmap_from_secstruct(new_struc)
match = SequenceMatcher(None,new_pm,target_pm).ratio()
for j in range(5):
for i in range(len(dot_bracket)):
if new_pm == target_pm:
print 'puzzle solved'
SOLVE = True
break
else:
if new_pm[i] == target_pm[i]:
continue
else:
paired = target_pm[i]
base1 = seq[i]
base2 = seq[paired]
if paired == -1: continue
seq[i] = base2
seq[paired] = base1
p = Popen(['../../../EteRNABot/eternabot/./RNAfold', '-T','37.0'], stdout=PIPE, stdin=PIPE, stderr=STDOUT)
pair = p.communicate(input=''.join(seq))[0]
formatted = re.split('\s+| \(?\s?',pair)
new_pm = get_pairmap_from_secstruct(formatted[1])
new_match = SequenceMatcher(None,new_pm,target_pm).ratio()
if new_match > match:
match = copy.deepcopy(new_match)
m.append([str_to_num(seq[i]),i+1])
m.append([str_to_num(seq[paired]),paired+1])
else:
seq[i] = base1
seq[paired] = base2
for i in range(len(dot_bracket)):
if new_pm[i] == target_pm[i]:
continue
else:
paired = target_pm[i]
seq[i] = 'G'
seq[paired] = 'C'
m.append([3,i+1])
m.append([4,paired+1])
for j in range(3):
for i in range(len(dot_bracket)):
if new_pm == target_pm:
print 'puzzle solved'
SOLVE = True
break
else:
if new_pm[i] == target_pm[i]:
continue
else:
paired = target_pm[i]
base1 = seq[i]
base2 = seq[paired]
if paired == -1: continue
seq[i] = base2
seq[paired] = base1
p = Popen(['../../../EteRNABot/eternabot/./RNAfold', '-T','37.0'], stdout=PIPE, stdin=PIPE, stderr=STDOUT)
pair = p.communicate(input=''.join(seq))[0]
formatted = re.split('\s+| \(?\s?',pair)
new_pm = get_pairmap_from_secstruct(formatted[1])
new_match = SequenceMatcher(None,new_pm,target_pm).ratio()
if new_match > match:
match = copy.deepcopy(new_match)
m.append([str_to_num(seq[i]),i+1])
m.append([str_to_num(seq[paired]),paired+1])
else:
seq[i] = base1
seq[paired] = base2
return ''.join(seq),m,SOLVE
cs,_ = RNA.fold(''.join(seq))
current_pm = get_pairmap_from_secstruct(cs)
