import os
import Ribozyme_generation
import Util_functions
import pickle
import shutil
# Load in the list of sequences to fold
struct_file = open('seq_list.pkl', 'rb')
full_list = pickle.load(struct_file)
# Get the structure of the native ribozyme for comparison
five_HHRz = 'GCUGUCACCGGAUGUGCUUUCCGGUCUGAUGAGUCCGU'
three_HHRz = 'GAGGACGAAACAGC'
[ribozyme_parts, loops] = Ribozyme_generation.RNAStructure_get_reference_structures(five_HHRz + three_HHRz,
'ribozyme', five_HHRz)
print([ribozyme_parts, loops])
tuple_list = []
bar = Util_functions.ProgressBar(len(full_list))
for seq in full_list:
if not os.path.exists("Test_ribozymes"):
os.makedirs("Test_ribozymes")
Ribozyme_generation.RNAStructure_minimal_generator(seq, 1, "Test_ribozymes/test")
# Iterates through each tested ribozyme structure(teststruct) and finds ribozyme active and aptamer formed.
testopen = open("Test_ribozymes/test.1.txt")
testopen = testopen.readlines()
# Gets the sequence of the loops for the sequence, if correctly folded.
teststruct = ''
if testopen != []:
teststruct = testopen[2][:-1]
[loops, stem_lengths] = Ribozyme_generation.get_ribozyme_loops(seq, teststruct, ribozyme_parts)
else:
[loops, stem_lengths] = [['', ''], [0, 0]]
shutil.rmtree("Test_ribozymes")
tuple_list.append((seq, [loops, stem_lengths], teststruct))
bar.update()
print(bar.get_bar())
print(bar.get_time_remaining())
# Dumps list of sequences, folded structure, and loop sequences to a pickle file for storage and later analysis.
struct_file = open('Candidate_list_RNAs_min_structures.pkl', 'wb')
pickle.dump(tuple_list, struct_file)
struct_file.close()