diff --git a/binary_dna_conversion.py b/binary_dna_conversion.py
index 98c63b7539c6b9588271108f9123761991ddd340..1510a0f0fc8a6f9587fac9f050918849f38b00e4 100755
--- a/binary_dna_conversion.py
+++ b/binary_dna_conversion.py
@@ -115,7 +115,7 @@ def dna_to_binary_abaab(sequence: str) -> str:
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
+ # a rest of 3 should not occur from a binary to dna abaab conversion, but a non coding base 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
@@ -188,27 +188,9 @@ def remove_ban_words_abaab_encoding(sequence: str, abaab_method_offset=0) -> str
exit(1)
return sequence_wo_bans
-
-
-def size_binary_from_dna_len_abaab(dna_length):
- """
- assume dna_abaab to binary conversion
- get the length the binary string will be from the given dna sequence
- conversion rate is 1.6bit/base
- """
- base_length = 8 * (dna_length//5) # full conversion of octets
- rest = dna_length % 5
- if rest == 0:
- return base_length
- if rest == 1:
- return base_length + 2
- if rest == 2 or rest == 3: # if rest of 3, act like a rest of 2 because the third base will be ignored
- return base_length + 4
- if rest == 4:
- return base_length + 6
-
+
-def size_of_dna_from_bit_len_abaab(bit_length):
+def size_dna_from_bit_len_abaab(bit_length):
"""
assume binary to dna_abaab conversion
get the size the dna sequence will be from the given binary string length
@@ -226,23 +208,42 @@ def size_of_dna_from_bit_len_abaab(bit_length):
return base_length + 4
print("error size_of_dna_from_bit_len : size not multiple of 2 :",str(bit_length))
exit(1)
-
+
+
+
+def size_binary_from_dna_len_abaab(dna_length):
+ """
+ assume dna_abaab to binary conversion
+ get the length the binary string will be from the given dna sequence
+ conversion rate is 1.6bit/base
+ """
+ base_length = 8 * (dna_length//5) # full conversion of octets
+ rest = dna_length % 5
+ if rest == 0:
+ return base_length
+ if rest == 1:
+ return base_length + 2
+ if rest == 2 or rest == 3: # if rest of 3, act like a rest of 2 because the third base will be ignored
+ return base_length + 4
+ if rest == 4:
+ return base_length + 6
+
def binary_to_dna_baa(binary_string: str, GC_window=20) -> str:
"""
convert binaries into dna sequence with some properties
the binaries are divided into parts of 5 bits
- for each 5 bits part, 1st 2nd bits are normally converted into dna : (00:A, 01:G, 10:T, 11:C)
- 3rd bit is converted depending on previous converted sequence :
- (0:G, 1:C) or (0:A, 1:T), first to break potential homopolymer, if not then to adjust %GC of the previous sequence
- 4th 5th bits are normally converted into dna
+ for each 5 bits part, 1st bit is converted depending on previous converted sequence :
+ (0:G, 1:C) or (0:A, 1:T), first to break potential homopolymer, if not then to adjust %GC of the local sequence in a defined window
+ 2nd 3rd bits are normally converted into dna : (00:A, 01:G, 10:T, 11:C)
+ 4th 5th bits are normally converted into dna : (00:A, 01:G, 10:T, 11:C)
this ensure that the total sequence cannot contain homopolymers > 3,
the GC% is in [33%, 66%] in the worst case in a window of 3, but tends to 50% with the adjustments and the conversion rate is 1.66 bit/base
warning : need the binary string to be a multiple of 5, or rest is inconsistent with decoding
ex : a rest of 0 -> A, a rest of 00 -> A
- so how to decode A ?
+ so how to decode a base A ?
only allowing rests multiple of 5 removes ambiguity (also possible 0, 1 or 3 modulo 5)
"""
@@ -400,6 +401,41 @@ def remove_ban_words_baa_encoding(sequence: str, baa_method_offset=0) -> str:
return sequence_wo_bans
+def size_dna_from_bit_len_baa(bit_length):
+ """
+ assume binary to dna_baa conversion
+ get the size the dna sequence will be from the given binary string length
+ conversion rate is 1.66 bit/base
+ """
+ base_length = 3 * (bit_length//5) # 5 bits -> 3 bases
+ rest = bit_length % 5
+ if rest == 0:
+ return base_length
+ if rest == 1:
+ return base_length + 1
+ if rest == 3:
+ return base_length + 2
+
+ print("error size_of_dna_from_bit_len : invalid rest size:",str(rest))
+ exit(1)
+
+
+def size_binary_from_dna_len_baa(dna_length):
+ """
+ assume dna_baa to binary conversion
+ get the length the binary string will be from the given dna sequence
+ conversion rate is 1.66 bit/base
+ """
+ base_length = 5 * (dna_length//3) # 3 bases -> 5 bits
+ rest = dna_length % 3
+ if rest == 0:
+ return base_length
+ if rest == 1:
+ return base_length + 1
+ if rest == 2:
+ return base_length + 3
+
+
def test_conversion():
for binary_size in range(100, 15000, 1):
@@ -417,13 +453,20 @@ def test_conversion():
#decoded_abaab = dna_to_binary_abaab(seq_abaab)
decoded_baa = dna_to_binary_baa(seq_baa)
+ if size_binary_from_dna_len_baa(len(seq_baa)) != len(random_binary):
+ print("dna",str(len(seq_baa)))
+ exit(0)
+ if size_dna_from_bit_len_baa(len(random_binary)) != len(seq_baa):
+ print("bin",str(len(random_binary)))
+ exit(0)
+
#print("check abaab encoding", str(decoded_abaab == random_binary))
- print("check baa encoding", str(decoded_baa == random_binary))
- if not (decoded_baa == random_binary and sequence_control.sequence_check(seq_baa, min_GC=40, max_GC=60, verbose=True)):
+ #print("check baa encoding", str(decoded_baa == random_binary))
+ """if not (decoded_baa == random_binary and sequence_control.sequence_check(seq_baa, min_GC=40, max_GC=60, verbose=True)):
#print(random_binary)
print(seq_baa)
#print(decoded_baa)
- exit(1)
+ exit(1)"""
#print("check abaab encoding")
#sequence_control.sanity_check(seq_abaab)