def setUp(self):
random.seed(30)
self.max_homopolymer = 3
self.repeat_length = 4
self.max_content = 0.6
self.sequences = [
"".join([index_base.get(random.randint(0, 3)) for _ in range(24)])
for _ in range(50)
]
def encode(self, bit_segments):
dna_sequences = []
for segment_index, bit_segment in enumerate(bit_segments):
dna_sequence = []
if len(bit_segment) % 2 != 0:
bit_segment = [0] + bit_segment
for position in range(0, len(bit_segment), 2):
dna_sequence.append(index_base.get(self.mapping_rules.index(bit_segment[position: position + 2])))
dna_sequences.append(dna_sequence)
if self.need_logs:
self.monitor.output(segment_index + 1, len(bit_segments))
return dna_sequences
def get_dna(self, seed, prng, bit_segments, header_size):
self.seed = seed
self.payload = None
self.chuck_indices = prng.get_src_blocks_wrap(seed)
for chuck_index in self.chuck_indices:
if self.payload is None:
self.payload = bit_segments[chuck_index]
else:
self.payload = list(
map(self.xor, self.payload, bit_segments[chuck_index]))
bit_list = self._get_seed_list(header_size) + self.payload
dna_sequence = []
for index in range(0, len(bit_list), 2):
dna_sequence.append(
index_base.get(bit_list[index] * 2 + bit_list[index + 1]))
return dna_sequence
def encode(self, bit_segments):
dna_sequences = []
for segment_index, bit_segment in enumerate(bit_segments):
dna_sequence = []
if len(bit_segment) % 2 != 0:
raise ValueError(
"The length of inputted binary segment must be divided by 2!"
)
for position in range(0, len(bit_segment), 2):
dna_sequence.append(
index_base.get(
self.mapping_rules.index(
bit_segment[position:position + 2])))
dna_sequences.append(dna_sequence)
if self.need_logs:
self.monitor.output(segment_index + 1, len(bit_segments))
return dna_sequences