correction of encoding error when rest

binary_dna_conversion.py

@@ -68,6 +68,9 @@ def binary_to_dna_abaab(binary_string: str) -> str:
     ex : a rest of 0 -> A, a rest of 00 -> A
     so how to decode A ?
     only allowing rests multiple of 2 removes ambiguity
+    
+    #TODO warning : if ending with bsaI -> end can currently be aa when a rest of 4 bits -> will break with banword removal
+
     """
     
     if len(binary_string) % 2 != 0:
@@ -227,12 +230,12 @@ def binary_to_dna_baa(binary_string: str, GC_window=20) -> str:
     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 ?
-    only allowing rests multiple of 5 removes ambiguity (also possible 0,1 or 3 modulo 5)
+    only allowing rests multiple of 5 removes ambiguity (also possible 0, 1 or 3 modulo 5)
 
     """
-    if len(binary_string) % 5 != 0:
-            print("error binary dna conversion, need a binary string multiple of 5")
-            exit(0)
+    if len(binary_string) % 5 not in [0, 1, 3]:
+            print("error binary dna conversion, need a binary string multiple of 5, or 1, 3 modulo 5")
+            return
     
     sequence = ""
     n_quintuplets, rest = divmod(len(binary_string), 5)
@@ -266,12 +269,12 @@ def binary_to_dna_baa(binary_string: str, GC_window=20) -> str:
 
     if len(bit_rest) > 0:
     # last conversions depends on the length of the rest, 1 bits = 1 base; 3 bits = 2 bases
-        if len(bit_rest) == 3:
+        if len(bit_rest) == 1:
+            nucleotide_2 = ""
+            homopolymere_check_bool = sequence[-3] == sequence[-2] == sequence[-1] 
+        else: # rest = 3
             nucleotide_2 = bit_pair_to_dna[bit_rest[1:3]] # nucleotide_2 from a pair of bits
             homopolymere_check_bool = sequence[-3] == sequence[-2] == sequence[-1] or sequence[-2] == sequence[-1] == nucleotide_2 # true => careful for a potential homopolymere
-        else:
-            nucleotide_2 = ""
-            homopolymere_check_bool = sequence[-3] == sequence[-2] == sequence[-1]
         
         if homopolymere_check_bool:
             # break homopolymere
@@ -281,9 +284,9 @@ def binary_to_dna_baa(binary_string: str, GC_window=20) -> str:
             # adjust GC%
             check_window = sequence[-min(len(sequence), GC_window):] + nucleotide_2
             if check_window.count("A")+check_window.count("T") > check_window.count("G")+check_window.count("C"):
-                nucleotide_1 = bit_to_dna_GC[bits5[0]]
+                nucleotide_1 = bit_to_dna_GC[bit_rest[0]]
             else:
-                nucleotide_1 = bit_to_dna_AT[bits5[0]]
+                nucleotide_1 = bit_to_dna_AT[bit_rest[0]]
                         
         sequence += nucleotide_1 + nucleotide_2
 
@@ -384,21 +387,27 @@ def remove_ban_words_baa_encoding(sequence: str, baa_method_offset=0) -> str:
 
 def test_conversion():
     
-    for binary_size in range(10,15000, 10):
-        print(binary_size)
+    for binary_size in range(10, 15000, 1):
+        print("size",str(binary_size))
         random_binary = ""
         for i in range(binary_size):
              random_binary += random.Random().choice(['0', '1'])
         
-        seq_abaab = binary_to_dna_abaab(random_binary)
+        #random_binary = "00011110010"
+        #seq_abaab = binary_to_dna_abaab(random_binary)
         seq_baa = binary_to_dna_baa(random_binary)
+        if seq_baa is None:
+            continue
         
-        decoded_abaab = dna_to_binary_abaab(seq_abaab)
+        #decoded_abaab = dna_to_binary_abaab(seq_abaab)
         decoded_baa = dna_to_binary_baa(seq_baa)
 
-        print("check abaab encoding", str(decoded_abaab == random_binary))
+        #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 decoded_abaab == random_binary ):
+        if not (decoded_baa == random_binary):
+            print(random_binary)
+            print(seq_baa)
+            print(decoded_baa)
             exit(1)
         
     #print("check abaab encoding")