diff --git a/binary_dna_conversion.py b/binary_dna_conversion.py
index bb2d2812607705ee47cbc783f629838702ede688..dbae39c05c02bbf4a87190109176c3601c33dd96 100755
--- a/binary_dna_conversion.py
+++ b/binary_dna_conversion.py
@@ -18,6 +18,16 @@ bit_to_dna_GC = {"0": "G", "1": "C"}
dna_to_bit_ATGC = {"A": "0", "T": "1", "G": "0", "C": "1", "_": "0"}
+def bit_to_dna_balance_GC(bit_char: str, reference_base: str):
+ """
+ convert a bit to a dna base to balance the GC with a reference base
+ """
+ if reference_base in ["A", "T"]:
+ return bit_to_dna_GC[bit_char]
+ else:
+ return bit_to_dna_AT[bit_char]
+
+
def binary_to_dna(binary_string: str) -> str:
"""
basic conversion of binaries into dna sequence
@@ -69,16 +79,14 @@ def binary_to_dna_abaab(binary_string: str) -> str:
for i in range(0, n_octets):
bits8 = binary_string[i*8:(i+1)*8]
nucleotide_1 = bit_pair_to_dna[bits8[0:2]]
- if nucleotide_1 in ["A", "T"]:
- nucleotide_2 = bit_to_dna_GC[bits8[2]]
- else:
- nucleotide_2 = bit_to_dna_AT[bits8[2]]
+
+ nucleotide_2 = bit_to_dna_balance_GC(bits8[2], nucleotide_1)
+
nucleotide_3 = bit_pair_to_dna[bits8[3:5]]
nucleotide_4 = bit_pair_to_dna[bits8[5:7]]
- if nucleotide_4 in ["A", "T"]:
- nucleotide_5 = bit_to_dna_GC[bits8[7]]
- else:
- nucleotide_5 = bit_to_dna_AT[bits8[7]]
+
+ nucleotide_5 = bit_to_dna_balance_GC(bits8[7], nucleotide_4)
+
sequence += nucleotide_1 + nucleotide_2 + nucleotide_3 + nucleotide_4 + nucleotide_5
# rest should be 0 because all documents contains a round number of octet
# but some "0" can be added to fill the fragments
@@ -91,10 +99,9 @@ def binary_to_dna_abaab(binary_string: str) -> str:
if len(bit_rest) == 4:
sequence += bit_pair_to_dna[bit_rest[2:4]] # nucleotide_2 also from a pair of bits
elif len(bit_rest) == 6:
- if nucleotide_1 in ["A", "T"]:
- sequence += bit_to_dna_GC[bit_rest[2]] # nucleotide_2 from a single bit and depending on nucleotide 1
- else:
- sequence += bit_to_dna_AT[bit_rest[2]] # nucleotide_2 from a single bit and depending on nucleotide 1
+
+ # nucleotide_2 from a single bit and depending on nucleotide 1
+ sequence += bit_to_dna_balance_GC(bit_rest[2], nucleotide_1)
sequence += bit_pair_to_dna[bit_rest[3:5]] # nucleotide_3 from a pair of bits
sequence += bit_to_dna_AT[bit_rest[5]] # nucleotide_4 from a single bit
@@ -240,10 +247,8 @@ def binary_to_dna_baa(binary_string: str, GC_window=20) -> str:
# check 3 previous encoded bases
if sequence[-3] == sequence[-2] == sequence[-1] or sequence[-2] == sequence[-1] == nucleotide_2 or sequence[-1] == nucleotide_2 == nucleotide_3:
# break homopolymere
- if sequence[-1] in ["A", "T"]:
- nucleotide_1 = bit_to_dna_GC[bits5[0]]
- else:
- nucleotide_1 = bit_to_dna_AT[bits5[0]]
+ nucleotide_1 = bit_to_dna_balance_GC(bits5[0], sequence[-1])
+
else:
# adjust GC% in the window of preceding bases + 2 new alpha bases
check_window = sequence[-min(len(sequence), GC_window):] + nucleotide_2 + nucleotide_3
@@ -253,10 +258,7 @@ def binary_to_dna_baa(binary_string: str, GC_window=20) -> str:
nucleotide_1 = bit_to_dna_AT[bits5[0]]
else:
- if nucleotide_2 in ["A", "T"]:
- nucleotide_1 = bit_to_dna_GC[bits5[0]]
- else:
- nucleotide_1 = bit_to_dna_AT[bits5[0]]
+ nucleotide_1 = bit_to_dna_balance_GC(bits5[0], nucleotide_2)
sequence += nucleotide_1 + nucleotide_2 + nucleotide_3
@@ -272,10 +274,8 @@ def binary_to_dna_baa(binary_string: str, GC_window=20) -> str:
if homopolymere_check_bool:
# break homopolymere
- if sequence[-1] in ["A", "T"]:
- nucleotide_1 = bit_to_dna_GC[bit_rest[0]]
- else:
- nucleotide_1 = bit_to_dna_AT[bit_rest[0]]
+ nucleotide_1 = bit_to_dna_balance_GC(bit_rest[0], sequence[-1])
+
else:
# adjust GC%
check_window = sequence[-min(len(sequence), GC_window):] + nucleotide_2
@@ -292,6 +292,41 @@ def binary_to_dna_baa(binary_string: str, GC_window=20) -> str:
return sequence_wo_banwords
+def dna_to_binary_abaab(sequence: str) -> str:
+ """
+ convert back a sequence to binaries (opposite of binary_to_dna_abaab)
+ """
+
+ binary_string = ""
+ n_quintuplet, rest = divmod(len(sequence), 5)
+ for i in range(0, n_quintuplet):
+ nucleotides5 = sequence[i*5:(i+1)*5]
+ bits_12 = dna_to_bit_pair[nucleotides5[0]]
+ bit_3 = dna_to_bit_ATGC[nucleotides5[1]]
+ bits_45 = dna_to_bit_pair[nucleotides5[2]]
+ bits_67 = dna_to_bit_pair[nucleotides5[3]]
+ bit_8 = dna_to_bit_ATGC[nucleotides5[4]]
+ binary_string += bits_12 + bit_3 + bits_45 + bits_67 + bit_8
+
+ # handle rest < 5
+ sequence_rest = sequence[n_quintuplet*5:n_quintuplet*5+rest]
+ if len(sequence_rest) >= 1: # 1 base -> 2 bits
+ binary_string += dna_to_bit_pair[sequence_rest[0]]
+
+ if len(sequence_rest) == 2: # 2 bases -> 2 bits + 2 bits
+ binary_string += dna_to_bit_pair[sequence_rest[1]]
+
+ elif len(sequence_rest) == 3:
+ # a rest of 3 should not occur from a binary to dna abaab conversion, but a non coding A can be added to get a round number of blocks
+ binary_string += dna_to_bit_pair[sequence_rest[1]] # just act like the rest was 2
+
+ elif len(sequence_rest) == 4: # 4 bases -> 2 bits + 1 bit + 2 bits + 1 bit
+ binary_string += dna_to_bit_ATGC[sequence_rest[1]] # 1 base -> 1 bit
+ binary_string += dna_to_bit_pair[sequence_rest[2]] # 1 base -> 2 bits
+ binary_string += dna_to_bit_ATGC[sequence_rest[3]] # 1 base -> 1 bit
+
+ return binary_string
+
def remove_ban_words_baa_encoding(sequence: str, baa_method_offset=0) -> str:
"""
remove banned words from a sequence encoded with the binary_conversion.binary_to_dna_baa() method