From 8201876a71c296e4e28e96fd13a794865c243440 Mon Sep 17 00:00:00 2001
From: oboulle <olivier.boulle@inria.fr>
Date: Fri, 21 Jul 2023 11:06:16 +0200
Subject: [PATCH] comments improved, refactoring
---
binary_dna_conversion.py | 43 +++++++++++++++++++++-------------------
1 file changed, 23 insertions(+), 20 deletions(-)
diff --git a/binary_dna_conversion.py b/binary_dna_conversion.py
index 4d4d790..77d56bc 100755
--- a/binary_dna_conversion.py
+++ b/binary_dna_conversion.py
@@ -272,46 +272,47 @@ def binary_to_dna_baa(binary_string: str, GC_window=20) -> str:
for i in range(0, n_quintuplets):
bits5 = binary_string[i*5:(i+1)*5]
- nucleotide_2 = bit_pair_to_dna[bits5[1:3]]
- nucleotide_3 = bit_pair_to_dna[bits5[3:5]]
+ nucleotide_2 = bit_pair_to_dna[bits5[1:3]] # first alpha base of the encoded triplet
+ nucleotide_3 = bit_pair_to_dna[bits5[3:5]] # 2nd alpha base
# make nucleotide 1
if len(sequence) >= 3:
- # check 3 previous encoded bases
+ # check 3 previous encoded bases and 2 following alpha bases to see if there is a potential homopolymer of 4+
if sequence[-3] == sequence[-2] == sequence[-1] or sequence[-2] == sequence[-1] == nucleotide_2 or sequence[-1] == nucleotide_2 == nucleotide_3:
- # break homopolymer
+ # break the homopolymer
nucleotide_1 = bit_to_dna_balance_GC(bits5[0], sequence[-1])
else:
- # if no homopolymer to break, adjust GC% in the window of preceding bases + 2 new alpha bases
+ # if no homopolymer to break, adjust GC% in the window of preceding bases + 2 following alpha bases
check_window = sequence[-min(len(sequence), GC_window):] + nucleotide_2 + nucleotide_3
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[bits5[0]] # more A/T -> add a G/C
elif check_window.count("A")+check_window.count("T") < check_window.count("G")+check_window.count("C"):
- nucleotide_1 = bit_to_dna_AT[bits5[0]]
- else: # strictly equal, just balance with preceding base
+ nucleotide_1 = bit_to_dna_AT[bits5[0]] # less A/T -> add a A/T
+ else: # case of strictly equal %GC, just balance with following base
nucleotide_1 = bit_to_dna_balance_GC(bits5[0], nucleotide_2)
- else:
+ else: # empty string, just balance the GC with the following base
nucleotide_1 = bit_to_dna_balance_GC(bits5[0], nucleotide_2)
- sequence += nucleotide_1 + nucleotide_2 + nucleotide_3
+ sequence += nucleotide_1 + nucleotide_2 + nucleotide_3 # add the encoded b a a bases to the sequence
- bit_rest = binary_string[n_quintuplets*5:n_quintuplets*5+rest] # rest is 0-1-3 bits
+ # all complete quintuplets have been encoded, time for the rest
+ bit_rest = binary_string[n_quintuplets*5:n_quintuplets*5+rest] # rest is 0-1-3 bits long
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) == 1:
- nucleotide_2 = ""
+ nucleotide_2 = "" # no nucleotide 2 to add
homopolymer_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
homopolymer_check_bool = sequence[-3] == sequence[-2] == sequence[-1] or sequence[-2] == sequence[-1] == nucleotide_2 # true => careful for a potential homopolymer
if homopolymer_check_bool:
- # break homopolymer
+ # need to break homopolymer with the nucleotide 1
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
@@ -319,9 +320,9 @@ def binary_to_dna_baa(binary_string: str, GC_window=20) -> str:
nucleotide_1 = bit_to_dna_GC[bit_rest[0]]
else:
nucleotide_1 = bit_to_dna_AT[bit_rest[0]]
-
+
sequence += nucleotide_1 + nucleotide_2
-
+
# remove the banned words
sequence_wo_banwords = remove_ban_words_baa_encoding(sequence)
@@ -336,10 +337,10 @@ def dna_to_binary_baa(sequence: str) -> str:
binary_string = ""
n_triplet, rest = divmod(len(sequence), 3)
for i in range(0, n_triplet):
- nucleotides3 = sequence[i*3:(i+1)*3]
- bit_1 = dna_to_bit_ATGC[nucleotides3[0]]
- bits_23 = dna_to_bit_pair[nucleotides3[1]]
- bits_45 = dna_to_bit_pair[nucleotides3[2]]
+ triplet_nucleotide = sequence[i*3:(i+1)*3]
+ bit_1 = dna_to_bit_ATGC[triplet_nucleotide[0]]
+ bits_23 = dna_to_bit_pair[triplet_nucleotide[1]]
+ bits_45 = dna_to_bit_pair[triplet_nucleotide[2]]
binary_string += bit_1 + bits_23 + bits_45
@@ -362,6 +363,8 @@ def remove_ban_words_baa_encoding(sequence: str, baa_method_offset=0) -> str:
the changed base must be a beta base, and be A<=>G; T<=>C, so the decoding of the updated sequence will still return the same result
if the original sequence has already been fragmented, the 3 bases windows of the baa method can be offset, baa_method_offset is used to correct this
+
+ #TODO also remove inverse repeat regions of 10+ bases
"""
# change a beta base but keep the binary meaning for the decoding
--
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