# parse *rnm files and create .pair file
rnm_files = glob.glob(KineFold_dir + "/*.rnm")
pair_dict = defaultdict(list)
seq_dict = {}
time_dict = defaultdict(list)
for rf in rnm_files:
# parse *rnm file for base pairs
if time_weight:
kf_dbns, kf_energy_path, kf_times = SU.get_rnm_structs_dbn(
rf, outdir, time_weight, simulation_time_ms)
else:
kf_dbns, kf_energy_path = SU.get_rnm_structs_dbn(rf, outdir)
if last_structure: # ignoring time spent because only considering structure at end of simulation
OSU.remove_files(kf_dbns[:-1])
kf_dbns = kf_dbns[-1:]
kf_energy_path = kf_energy_path[-1:]
for i in range(len(kf_dbns)):
seq, struct = read_dbn(kf_dbns[i])
nt_length = len(seq)
pairs = dbn_to_pairs(struct)
pair_dict[nt_length].append(pairs)
seq_dict[nt_length] = seq
OSU.remove_file(kf_dbns[i])
if time_weight:
time_dict[nt_length].append(kf_times[i])
# Edited from Paul Gasper's pairs_from_dbn_2.py
for key in seq_dict.keys():
with open('{0}/{1}nt.pairs'.format(outdir, key), 'w') as out_fh:
import LucksLabUtils_config
import glob
# setup environment variables
LucksLabUtils_config.config("Quest_R2D2")
opts = OSU.getopts("o:", ["dbn_dir=", "out_prefix="])
print opts
output_dir = OSU.create_directory(opts['-o'])
dbn_dir = opts['--dbn_dir']
out_prefix = opts['--out_prefix']
dbns = {}
for dbnf in glob.glob(dbn_dir + "/*.dbn"):
# read in each rho reactivitiy spectra
with open(dbnf, "r") as f:
dbn = f.readlines()[-1].strip() # last line with dotbracket
SU.run_dot2ct(dbnf, output_dir + "temp.ct")
SU.runRNAstructure_efn2(output_dir + "temp.ct",
output_dir + "temp.efn2",
parallel=False)
dg = SU.get_free_energy_efn2(output_dir + "temp.efn2")[0]
dbns[len(dbn)] = dg # save in dict, nt : DG
OSU.remove_files([output_dir + "temp.ct", output_dir + "temp.efn2"])
with open(output_dir + out_prefix + "_DG.dump", "w") as f:
f.write("\t".join(["nt", "DG", "consensus"]) + "\n")
for key in sorted(dbns):
f.write("\t".join([str(key), str(dbns[key]), "1"]) + "\n")
structs_pickle_dir + "temp_c%s.seq" % (str(constrain_val)))
sampled_counts, sampled = SU.RNAstructure_sample(
reactivities[k][2],
sample_n,
structs_pickle_dir,
seqfile,
shapefile="",
constraintfile=structs_pickle_dir + "/temp_c%s.con" %
(str(constrain_val)),
label="constrain_" + str(constrain_val),
num_proc=1,
shape_slope=shape_slope,
shape_intercept=shape_intercept)
constrained_folds[k] = sampled
OSU.remove_files([
structs_pickle_dir + "/temp_c%s.con" % (str(constrain_val)),
structs_pickle_dir + "temp_c%s.seq" % (str(constrain_val))
])
pickle.dump(
constrained_folds,
open(
"%sconstrained_folds_%s.p" %
(structs_pickle_dir, str(constrain_val)), "wb"))
else:
with open(structs_pickle_dir + "/save_crystals.p", "rb") as f:
crytals = pickle.load(f)
with open(structs_pickle_dir + "/save_reactivities.p", "rb") as f:
reactivities = pickle.load(f)
# handle rho_midpoints if cap_rhos is False
if not cap_rhos:
rho_midpoints = [-1.0]