fasta_file = FASTA(sys.argv[1])
fasta_file.read()
alphabet = list(set(fasta_file.data))
alphabet.sort()
tree = WaveletTree()
tree.build(alphabet, fasta_file.data)
if task == 'access':
index = int(sys.argv[4])
result = tree.access(index)
elif task == 'rank':
position = int(sys.argv[4])
character = sys.argv[5]
result = tree.rank(position, character)
elif task == 'select':
nth_occurence = int(sys.argv[4])
character = sys.argv[5]
result = tree.select(nth_occurence, character)
elif task == 'build':
result = 'OK'
# Save result to out file
out_file = open(sys.argv[2], 'w')
out_file.write(str(result))
out_file.close()
fasta_file = FASTA(sys.argv[1])
fasta_file.read()
alphabet = list(set(fasta_file.data))
alphabet.sort()
tree = WaveletTree()
tree.build(alphabet, fasta_file.data)
if task == 'access':
index = int(sys.argv[4])
result = tree.access(index)
elif task == 'rank':
position = int(sys.argv[4])
character = sys.argv[5]
result = tree.rank(position, character)
elif task == 'select':
nth_occurence = int(sys.argv[4])
character = sys.argv[5]
result = tree.select(nth_occurence, character)
elif task == 'build':
result = 'OK'
# Save result to out file
out_file = open(sys.argv[2], 'w')
out_file.write(str(result))
out_file.close()
# Access
stopwatch.restart()
stopwatch.start()
tree.access(test_idx)
stopwatch.stop()
time_access = time_access + stopwatch.elapsed_ms()
# Select
stopwatch.restart()
stopwatch.start()
tree.select(test_nth_occurence, test_character)
stopwatch.stop()
time_select = time_select + stopwatch.elapsed_ms()
stopwatch.restart()
# Rank
stopwatch.start()
tree.rank(test_idx, test_character)
stopwatch.stop()
time_rank += stopwatch.elapsed_ms()
time_select /= test_runs
time_rank /= test_runs
time_access /= test_runs
report_3(read_stopwatch, build_stopwatch, time_select, time_rank,
time_access)
else:
report_2(read_stopwatch, build_stopwatch)
# Access
stopwatch.restart()
stopwatch.start()
tree.access(test_idx)
stopwatch.stop()
time_access = time_access + stopwatch.elapsed_ms()
# Select
stopwatch.restart()
stopwatch.start()
tree.select(test_nth_occurence, test_character)
stopwatch.stop()
time_select = time_select + stopwatch.elapsed_ms()
stopwatch.restart()
# Rank
stopwatch.start()
tree.rank(test_idx, test_character)
stopwatch.stop()
time_rank += stopwatch.elapsed_ms()
time_select /= test_runs
time_rank /= test_runs
time_access /= test_runs
report_3(read_stopwatch, build_stopwatch, time_select, time_rank, time_access)
else:
report_2(read_stopwatch, build_stopwatch)
