def duplex2_energy(s):
s = 'c' + s[1] + 'GCgaaaGC' + s[0] + 'c'
ss = '((((....))))'
from rna_tools.Seq import RNASequence
seq = RNASequence(s)
en, ss, comment = seq.predict_ss('mcfold', constraints=ss)
# print(' ', s, en, ss)
return en
def duplex_energy(s):
"""
cGAUCgaaaGAUCg
(((((....)))))
rna_secondary_structure_prediction.py --method mcfold --file wt.fa
"""
s = 'cG' + s[1] + 'GCgaaaGC' + s[0] + 'Cg'
ss = '(((((....)))))'
from rna_tools.Seq import RNASequence
seq = RNASequence(s)
en, ss, comment = seq.predict_ss('mcfold', constraints=ss)
print(' ', s, en, ss)
return en
cst = f.readline().strip()
assert cst, 'Cst line empty, check the input file'
try:
print(seq)
except NameError:
parser.print_usage()
parser.exit(1)
if args.cst:
cst = args.cst
if cst:
print(cst, '<= cst')
if args.method == 'cyclefold':
seq = RNASequence(seq)
ss, en = seq.predict_ss('rnastructure_CycleFold', verbose=args.verbose)
print(en, ss)
if args.method == 'mcfold':
seq = RNASequence(seq)
if cst:
en, ss, comment = seq.predict_ss('mcfold',
constraints=cst,
verbose=args.verbose)
else:
en, ss, comment = seq.predict_ss(method='mcfold',
verbose=args.verbose)
#if not ss:
# ss = 'x'
print(ss, en)
#!/usr/bin/python
#-*- coding: utf-8 -*-
from rna_tools.Seq import RNASequence
seq = RNASequence("CCuuuuGG")
print(seq.predict_ss("mcfold", verbose=True))
seq = RNASequence("CCuuuuGG")
print(seq.predict_ss("mcfold", constraints='(......)', verbose=True))
import rna_tools.tools.rna_alignment.rna_alignment as ra
alignment = ra.RNAalignment('../input/RF02679_pistol_stockholm.txt')
for s in alignment:
s.remove_gaps()
print(s)
print(s.seq)
print(s.ss)
# hack
s2 = RNASequence(s.seq, s.ss)
ss = s2.predict_ss(method='mcfold', constraints=s.ss.replace('.', '*'), verbose=True)
print(ss)
break
seq = 'acucggcuaggcgaguauaaauagccgucaggccuagcgcguccaagccuagccccuucuggggcugggcgaagggucggg'
ss = '((((........)))).......((((..............(((((((((((((((....)))))))))))))))..))))'
s = RNASequence(seq, ss)
print(s)
cst1 = "((((........)))).......((((..............(((((((((((((((....)))))))))))))))..))))"
cst2 = "((((........)))).......((((..............((((((((((..............))))))))))..))))"
# What to show? sst (from .cet file) of ss processed with RPT
if args.template:
log.info(sst)
else:
log.info(seq.ss)
if 'N' in seq.seq: # + 'N':
skipped += 1
continue # skip a seq with N
method = args.method
c = 1
dfrow = ''
for cst in cstl:
seqq = RNASequence(seq.seq)
# ech, remove gaps, but this RNASequence is not the same as RNASeq from the alignment
seqq.seq = seqq.seq.replace('-', '')
cst = cst.replace('-', '').strip()
if len(cst) != len(seqq.seq):
continue
energy, ss = seqq.predict_ss(method,
constraints=cst,
verbose=args.debug)
log.info(ss + ' ' + str(energy) + ' ' + cst)
energy_lower = energy
df = df.append(
{
'id': seq,
'ss': ss,
#!/usr/bin/python
from rna_tools.Seq import RNASequence
from rna_tools.rna_tools_config import CONTEXTFOLD_PATH, RNASTRUCTURE_PATH
seq = RNASequence(
"CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUAAAUAUCAGgUGCAA")
print(seq.predict_ss("rnastructure_CycleFold", verbose=True))
#!/usr/bin/python
#-*- coding: utf-8 -*-
from rna_tools.Seq import RNASequence
seq = RNASequence("CCuuuuGG")
print(seq.predict_ss("mcfold", verbose=True))
seq = RNASequence("CCuuuuGG")
print(seq.predict_ss("mcfold", constraints='(......)', verbose=True))
cst = cst_a + cst_l + cst_b
if args.flanks:
a = args.flanks[0] + a
b += args.flanks[1]
cst = '(' + cst + ')'
log.info(a + ' ' + loop_lower + ' ' + b)
log.info('')
log.info(a + loop_lower + b)
log.info(cst + ' <= cst')
# log.info('\_ loop lower: %s' % loop_lower)
seql = RNASequence(a + loop_lower + b)
#if '-' in seqn.seq: # + 'N':
# skipped_with_gaps += 1
# continue # skip a seq with N
#log.info(seql)
energy, ss = seql.predict_ss(method,
constraints=cst,
verbose=args.debug)
log.info(seql.seq + '\n' + ss + ' ' + str(energy))
energy_lower = energy
log.info('upper ------------------------------------')
## if args.loop_seq:
## loop_upper = seq.seq[9:14].lower() # # from alignment
## assert loop_upper, 'Loop is empty'
## else:
cst = f.readline().strip()
assert cst, 'Cst line empty, check the input file'
try:
print(seq_string)
except NameError:
parser.print_usage()
parser.exit(1)
if args.cst:
cst = args.cst
if cst:
print(cst, '<= cst')
if args.method == 'rnaeval' or args.method == 'all':
seq = RNASequence(seq_string)
energy = seq.eval(cst, verbose=args.verbose)
print('rnaeval:', energy)
if args.method == 'mcfold' or args.method == 'all':
seq = RNASequence(seq_string)
if cst:
en, ss, comment = seq.predict_ss('mcfold',
constraints=cst,
verbose=args.verbose)
else:
en, ss, comment = seq.predict_ss('mcfold',
verbose=args.verbose)
#if not ss:
# ss = 'x'
print('mcfold:', en, comment)
#!/usr/bin/python
from rna_tools.Seq import RNASequence
from rna_tools.rna_tools_config import CONTEXTFOLD_PATH, RNASTRUCTURE_PATH
seq = RNASequence("CGUGGUUAGGGCCACGUUAAAUAGUUGCUUAAGCCCUAAGCGUUGAUAAAUAUCAGgUGCAA")
print(seq.predict_ss("rnastructure_CycleFold", verbose=True))
a = ungap(seq[0:4])
b = ungap(seq[-3:])
####################
# to the new alignment send only a + b, overwrite the original sequence
# print(seq)
seq = a + '-' + b
# print(seq)
if args.u5:
a = ungap(seq[0:8])
b = ungap(seq[-9:])
seq = a + '-' + b
if args.calc_energy:
# u5
seql = RNASequence(seq.replace('-','').replace('N', 'u'))
cst = "((((((((...........))))))))"
#AAAUCUUUCGCCUUUUACUAAAGA-UUU
#((((((((...........))))).)))
energy, ss = seql.predict_ss(method="mcfold", constraints=cst, verbose=args.verbose)
# u6
#pass
## # u6atac
## a = 'g' + ungap(seq[0:5])
## b = ungap(seq[-4:]) + 'c'
## loop = "guaa"
## seql = RNASequence(a + loop + b)
## cst = '((((.((..))))))'
## if args.verbose:
## print('seq %s' % seq)
## print(a + loop + b)
a = ungap(seq[0:4])
b = ungap(seq[-3:])
####################
# to the new alignment send only a + b, overwrite the original sequence
# print(seq)
seq = a + '-' + b
# print(seq)
if args.u5:
a = ungap(seq[0:8])
b = ungap(seq[-9:])
seq = a + '-' + b
if args.calc_energy:
# u5
seql = RNASequence(seq.replace('-', '').replace('N', 'u'))
cst = "((((((((...........))))))))"
#AAAUCUUUCGCCUUUUACUAAAGA-UUU
#((((((((...........))))).)))
energy, ss = seql.predict_ss(method="mcfold",
constraints=cst,
verbose=args.verbose)
# u6
#pass
## # u6atac
## a = 'g' + ungap(seq[0:5])
## b = ungap(seq[-4:]) + 'c'
## loop = "guaa"
## seql = RNASequence(a + loop + b)
## cst = '((((.((..))))))'
## if args.verbose:
from rna_tools.Seq import RNASequence seq = "AGUCGUUGUGGCGACUAUAACCAAGCUCUUUAAGCCACAAGCGUUGCUGAUGAGGUUUCAUAACAUCAGCAGGUAGAG" ss = "((((..[[[[[.)))).........((((.....]]]]]....(((((((((...........)))))))))..))))" s = RNASequence(seq, ss) print(s.predict_ss(method='mcfold', constraints=ss, verbose=True)) ss = "((((..[[[[[.)))).........((((.....]]]]]....(((((((((***********)))))))))..))))" print(s.predict_ss(method='mcfold', constraints=ss, verbose=True))
if __name__ == '__main__':
args = get_parser().parse_args()
a = RNAalignment(args.file)
target_seq = ''
df = pd.DataFrame()
for s in a:
if 'XX' in s.seq: # skip line with X
continue
if not target_seq:
target_seq = s.seq
dist = s.get_distance_to(target_seq)
s.remove_gaps()
length = len(s)
s2 = RNASequence(s.seq, s.ss)
cst = s.ss
if args.all_stars:
cst = s.ss.replace('.', '*')
explore = 1
else:
explore = ''
if not args.skip_mcfold:
ss = list(
s2.predict_ss(method='mcfold',
constraints=cst,
explore=explore,
verbose=args.verbose))
ss[0] = str(ss[0]) # str first value
if args.verbose: print(ss)
else: