def test_decodability(args):
e_correction = args[0]
repair_symbols = int(args[1])
cmp_str = b"AAAAAACHZACHEFAKLF(24z98"
assert get_error_correction_decode(e_correction, repair_symbols)(
get_error_correction_encode(e_correction,
repair_symbols)(cmp_str)) == cmp_str
required=False,
type=bool,
default=False)
parser.add_argument("--save_number_of_chunks",
metavar="save_number_of_chunks",
required=False,
type=bool,
default=False)
parser.add_argument("--as_mode_1_bmp", required=False, action="store_true")
overhead = 6.0
args = parser.parse_args()
arg_file = args.filename
arg_chunk_size = args.chunk_size
arg_number_of_chunks = args.number_of_chunks
arg_as_dna = args.as_dna
e_correction = args.error_correction
norepair_symbols = args.repair_symbols
arg_insert_header = args.insert_header
save_number_of_chunks = args.save_number_of_chunks
arg_mode_1_bmp = args.as_mode_1_bmp
if arg_chunk_size == arg_number_of_chunks == 0:
print("Please set either a chunk_size or a number_of_chunks")
exit()
arg_error_correction = get_error_correction_encode(e_correction,
norepair_symbols)
print("File to encode: " + str(arg_file))
main(arg_file, arg_number_of_chunks, arg_chunk_size, arg_as_dna,
arg_error_correction, arg_insert_header, save_number_of_chunks,
arg_mode_1_bmp)
print("File encoded.")
parser.add_argument("--drop_upper_bound", metavar="drop_upper_bound", required=False, type=float, default=0.5,
help="upper bound for calculated error probability of packet before dropping")
parser.add_argument("--overhead", metavar="overhead", required=False, type=float, default=0.40,
help="desired overhead of packets")
parser.add_argument("--epsilon", metavar="epsilon", required=False, type=float, default=0.068,
help="epsilon value of the coding")
parser.add_argument("--quality", metavar="quality", required=False, type=int, default=7,
help="quality value of the coding")
args = parser.parse_args()
_file = args.filename
#_chunk_size = args.chunk_size
_no_repair_symbols = args.repair_symbols
_insert_header = args.insert_header
_save_number_of_chunks = args.save_number_of_chunks
_upper_bound = args.drop_upper_bound
_error_correction = get_error_correction_encode(args.error_correction, _no_repair_symbols)
_save_as_fasta = args.save_as_fasta
_save_as_zip = args.save_as_zip
_overhead = args.overhead
_epsilon = args.epsilon
_quality = args.quality
# for _file in input_files:
print("File to encode: " + str(_file))
demo = demo_online_encode()
encoder_instance = demo.encode(_file, error_correction=_error_correction,
insert_header=_insert_header, save_number_of_chunks_in_packet=_save_number_of_chunks,
save_as_fasta=_save_as_fasta, save_as_zip=_save_as_zip, overhead=_overhead,
epsilon=_epsilon, quality=_quality, upper_bound=_upper_bound)
conf = {'error_correction': args.error_correction, 'repair_symbols': _no_repair_symbols, 'asdna': True,
'number_of_splits': 0, 'quality': encoder_instance.quality, 'epsilon': encoder_instance.epsilon,
'find_minimum_mode': False, 'seq_seed': False}
def plot_numbers(counter: typing.List[int], save_str):
plt.plot(counter)
plt.xlabel("Chunk")
plt.ylabel("# Occurrences")
plt.savefig(save_str + '.svg')
if __name__ == "__main__":
file = "logo.jpg"
number_of_chunks = 400
insert_header = True
rules = FastDNARules()
norepair_symbols = 4
error_correction_str = "reedsolomon"
error_correction = get_error_correction_encode(error_correction_str, norepair_symbols)
PACKET_LEN_FORMAT = "I"
CRC_LEN_FORMAT = "I"
NUMBER_OF_CHUNKS_LEN_FORMAT = "I"
ID_LEN_FORMAT = "I"
save_number_of_chunks_in_packet = False
upper_bound = 0.9
encoder = RU10Encoder(file, number_of_chunks, RaptorDistribution(number_of_chunks=number_of_chunks),
insert_header=insert_header, pseudo_decoder=None,
chunk_size=0, rules=rules, error_correction=error_correction,
packet_len_format=PACKET_LEN_FORMAT,
crc_len_format=CRC_LEN_FORMAT, number_of_chunks_len_format=NUMBER_OF_CHUNKS_LEN_FORMAT,
id_len_format=ID_LEN_FORMAT, save_number_of_chunks_in_packet=save_number_of_chunks_in_packet,
mode_1_bmp=False, prepend="", append="", drop_upper_bound=upper_bound)
encoder.set_overhead_limit(0.40)
# encoder.encode_to_packets()