# ============================ IMPORTS ====================================
import subprocess
import time
import resource

# take a RNA sequence and cut it from 100 bases to actual length
# then measure computation time, peak memory, and number of solutions for each length

# This RNA is actually a 16S rRNA from PDB 1J5E.
# http://ndbserver.rutgers.edu/service/ndb/atlas/summary
seq = "UUUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU"

step = 100
n = len(seq)

while step < len(seq)+50:
	sub_seq = seq[0:(min(step,n))]

	# write the sequence to file
	fasta = open("data/fasta/ZDFS33.fa", 'w')
	fasta.write(">__'ZDFS33 : 0-" + str(len(sub_seq)) + "'\n" + sub_seq)
	fasta.close()

	# run biorseo on it, with default options
	cmd = ["./bin/biorseo", "-d", "./data/modules/DESC", "-s", "data/fasta/ZDFS33.fa", "-v"]
	old_time = time.time()
	output = subprocess.check_output(cmd, stderr=subprocess.DEVNULL).decode("utf-8").split("\n")[-5:]
	run_time = time.time() - old_time
	max_ram = resource.getrusage(resource.RUSAGE_CHILDREN).ru_maxrss

	for line in output :
		if "Quitting because combinatorial issues" in line :
			nb_sol = -1
		elif "solutions kept" in line :
			nb_sol = line.split(",")[1].split()[0]

	print(len(sub_seq), "first nucleotides :", nb_sol, "solutions in", run_time, "seconds, using", max_ram, "kb of RAM")

	step += 50