diff --git a/binary_dna_conversion.py b/binary_dna_conversion.py
index 1510a0f0fc8a6f9587fac9f050918849f38b00e4..b2a9b726b2d50abe6149cfe9916091d1164e8942 100755
--- a/binary_dna_conversion.py
+++ b/binary_dna_conversion.py
@@ -206,7 +206,7 @@ def size_dna_from_bit_len_abaab(bit_length):
return base_length + 2
if rest == 6:
return base_length + 4
- print("error size_of_dna_from_bit_len : size not multiple of 2 :",str(bit_length))
+ print("error size_of_dna_from_bit_len_abaab : size not multiple of 2 :",str(bit_length))
exit(1)
diff --git a/file_to_dna.py b/file_to_dna.py
index b6a041d07bddc75a4b1ff613e758967d98dfd574..baab5a37094805ea64a40bb2af1e09bc1d002248 100755
--- a/file_to_dna.py
+++ b/file_to_dna.py
@@ -13,6 +13,7 @@ import dna_file_reader as dfr
"""
Can be used to convert any type of file
use the byte encoding of the file to convert to a dna sequence
+the file need to have a round number of octets
a single substitution error in the sequences can lead to a corrupted file (except for .txt files)
"""
@@ -30,7 +31,6 @@ intern_extremity_size = overhang_size + bsaI_size + buffer_size # size of non-pa
max_total_block_size = 300 # maximum allowed size for a complete block
min_total_block_size = 300 # minimum allowed size for a complete block
-force_size_to_max = True # set to false if blocks can have any size between min and max, else force the size of all blocks to be the max size
n_block_max = 10 # maximum assembled number of blocks
@@ -113,6 +113,7 @@ def encode_file(input_path: str, output_path: str) -> None:
"""
binary_string = convert_file_to_bits(input_path) # get the binary string representing the file content
+ #binary_string = input_path #TODO REMOVE
dna_payload_size = bdc.size_dna_from_bit_len_abaab(len(binary_string) + CHECK_SUM_SIZE) # length of the payload after conversion in dna
#print("payload size",str(dna_payload_size))
@@ -125,42 +126,31 @@ def encode_file(input_path: str, output_path: str) -> None:
print("error file to dna : block number too high :",str(block_number),"for",input_path)
exit(1)
- # size of non payload dna part that is contained in the blocks
- dna_non_payload_size = 2*extern_extremity_size + 2*(block_number-1)*intern_extremity_size
+ # size of non payload dna part that is contained in the blocks and used for the assembly
+ dna_for_assembly_size = 2*extern_extremity_size + 2*(block_number-1)*intern_extremity_size
# estimate the total dna sequence length after addition of non coding parts
- total_dna_size = dna_payload_size + dna_non_payload_size
+ total_dna_size = dna_payload_size + dna_for_assembly_size
#print("total_dna_size",str(total_dna_size))
- if block_number == 1 and total_dna_size < min_total_block_size:
- #TODO fill the block
- print("error file to dna : 1 block too short", str(total_dna_size))
- exit(1)
- pass
-
- # add a non coding base at the end of the sequence to make the last block at correct size when it is not possible to do by adding bits of 0 (very rare case)
+ # possibility to add a non coding base at the end of the sequence to make the last block at correct size when it is not possible to do by adding bits of 0 (very rare case)
add_base_at_end = False
-
- if force_size_to_max or total_dna_size % block_number > 0: # need to add non payload bits to adjust the size of blocks
+ # round the number of base per blocks, make sure it is above the minimal block size
+ final_assembly_size = block_number * max(math.ceil(total_dna_size / block_number), min_total_block_size)
- # all blocks must be the maximum size
- if force_size_to_max: # find the next length the total sequence needs to be to have a division in blocks of maximum size
- final_assembly_size = block_number * max_total_block_size
- else: # all blocks still need to have the same round size
- # find the next length the total sequence needs to be to have equal division in blocks
- final_assembly_size = block_number * math.ceil(total_dna_size / block_number)
- #print("final_assembly_size",str(final_assembly_size))
-
- # calculate the number of bits to add to get a round number of equal length blocks
- dna_payload_needed_size = final_assembly_size - dna_non_payload_size
+ # case when some bits need to be added to increase the number of bases
+ if final_assembly_size != total_dna_size:
+
+ # calculate the number of bases to add to the payload to get a round number of equal length blocks
+ dna_payload_needed_size = final_assembly_size - dna_for_assembly_size
#print(bdc.size_binary_from_dna_len_abaab(dna_payload_needed_size) )
+ # get number of bits to add
filler_length = bdc.size_binary_from_dna_len_abaab(dna_payload_needed_size) - len(binary_string) - CHECK_SUM_SIZE
#print("dna_payload_needed_size",str(dna_payload_needed_size)," +",filler_length,"bits")
# fill with '0' at the beginning of the binary # not the end because some zip can end with octets of 0, which makes difficult to remove only the non coding '0'
binary_string = math.ceil(filler_length) * "0" + binary_string
-
#print("updated binary size", str(len(binary_string)))
# rare case where adding 0 can not solve the problem of round blocks
@@ -184,7 +174,7 @@ def encode_file(input_path: str, output_path: str) -> None:
if add_base_at_end: sequence += bdc.bit_to_dna_balance_GC("0", sequence[-1]) # add a non coding base different from the preceding one
- total_sequence_size = len(sequence)+ dna_non_payload_size
+ total_sequence_size = len(sequence)+ dna_for_assembly_size
# test for errors that should never occur (I hope ...)
# round number of blocks, no blocks too large, no blocks to small
@@ -193,10 +183,8 @@ def encode_file(input_path: str, output_path: str) -> None:
print("\tseq payload size",str(len(sequence)))
print("\ttotal estimated seq size",total_sequence_size)
print("\t",str(block_number),"blocks of",str(total_sequence_size/block_number))
- print("TODO remove me")
- #TODO
- return
exit(1)
+ #print("\t",str(block_number),"blocks of",str(total_sequence_size/block_number))
# split the sequence into blocks of correct size to add the non payload stuff later # start the block count at 1
sub_sequences_dict = {}
@@ -223,9 +211,11 @@ def encode_file(input_path: str, output_path: str) -> None:
# add number and blocks size to path, add type
output_path = output_path + "_" + str(block_number) + "x" + str(total_sequence_size//block_number) + ".fasta"
+ #return sequence #TODO REMOVE
+
dfr.save_dict_to_fasta(sub_sequences_dict, output_path)
-
+
def decode_file(input_path: str, output_path: str) -> None:
"""
@@ -236,7 +226,8 @@ def decode_file(input_path: str, output_path: str) -> None:
sub_sequences_dict = dfr.read_fasta(input_path)
sequence = "".join(sub_sequences_dict.values())
-
+ #sequence = input_path
+
# convert the dna sequence into a binary string
binary_from_dna_string = bdc.dna_to_binary_abaab(sequence)
@@ -266,6 +257,8 @@ def decode_file(input_path: str, output_path: str) -> None:
while binary_string.startswith(8*"0"): # 1/256 (2**8) chance to remove actual data ! but 8*0 is ascii char NULL
binary_string = binary_string[8:]
+ #return binary_string #TODO REMOVE
+
# convert binaries into bytes
n = int(binary_string, 2)
bytes = n.to_bytes((n.bit_length() + 7) // 8, 'big')
@@ -281,18 +274,23 @@ if __name__ == '__main__':
#binary_string = sys.argv[1]
#seq = encode_file(doc_path)
- print(get_max_binary_len())
- exit(0)
- for i in range(0,300000):
- """binary = str(bin(i))[2:]
+ #print(get_max_binary_len())
+ #exit(0)
- print(compute_check_sum(binary), calculate_check_sum2(binary), compute_check_sum(binary) == calculate_check_sum2(binary))
- if not compute_check_sum(binary) == calculate_check_sum2(binary):
- exit(1)"""
- #print("")
+ for i in range(400,10000, 8):
+ binary = i*"1"
+ if len(binary) % 2 != 0:
+ continue
+
print("i=",str(i))
- seq = encode_file("toto", i)
- decode_file(seq, "toto")
+ seq = encode_file("", binary)
+ binary_result = decode_file(seq, "toto")
+
+ if binary != binary_result:
+ #print(binary)
+ #print(seq)
+ #print(binary_result)
+ exit(0)
#encode_file("", "test")
#seq = binary_to_dna_abaab(binary_string)
#print(seq)