Python: How to encode DNA sequence using binary values?

Tags: , , , ,



I would like to convert a file that contained few DNA sequences into binary values which is as follow:

A=1000
C=0100
G=0010
T=0001

FileA.txt

CCGAT
GCTTA

Desired output

01000100001010000001
00100100000100011000

I have tried using this code to solve my problem but the bin output file seem failed to output my desired answer. Can anyone help me?

Code

import sys

if len(sys.argv) != 2 :
  sys.stderr.write('Usage: {} <nucleotide file>n'.format(sys.argv[0]))
  sys.exit()

# assumes the file only contains dna and newlines
sequence = ''
for line in open(sys.argv[1]) :
  sequence += line.strip().upper()

sequence = sequence.replace('A', chr(0b1000))
sequence = sequence.replace('C', chr(0b0100))
sequence = sequence.replace('G', chr(0b0010))
sequence = sequence.replace('T', chr(0b0001))

outfile = open(sys.argv[1] + '.bin', 'wb')

outfile.write(bytearray(sequence, encoding = 'utf-8'))

Answer

Do you want ascii output or binary? The below will give you what you show in your post (though on a single line. Code needs to be modified to keep newlines).

import sys

if len(sys.argv) != 2 :
  sys.stderr.write('Usage: {} <nucleotide file>n'.format(sys.argv[0]))
  sys.exit()

# assumes the file only contains dna and newlines
sequence = ''
for line in open(sys.argv[1]) :
  sequence += line.strip().upper()

sequence = sequence.replace('A', '1000')
sequence = sequence.replace('C', '0100')
sequence = sequence.replace('G', '0010')
sequence = sequence.replace('T', '0001')

outfile = open(sys.argv[1] + '.bin', 'wb')

outfile.write(sequence)

EDIT This creates a binary file where each nucleotide is a byte and the newlines are preserved in binary format.

import sys

if len(sys.argv) != 2 :
  sys.stderr.write('Usage: {} <nucleotide file>n'.format(sys.argv[0]))
  sys.exit()

# assumes the file only contains dna and newlines
newbytearray=bytearray(b'',encoding='utf-8')
dict={'A':0b1000,'C':0b0100,'G':0b0010,'T':0b0001,'n':0b1010}
with open(sys.argv[1]) as file:
    while True:
        char=file.read(1)
        if not char:
            file.close()
            break
        newbytearray.append(dict[char])
outfile = open(sys.argv[1] + '.bin', 'wb')
outfile.write(newbytearray)
outfile.close()

#Converts the binary file to unicode and prints the result sequence.
testBin = open('fileA.txt.bin','rb')
sequence=''
for line in testBin:
    line = line.replace(chr(0b1000),'1000')
    line = line.replace(chr(0b0100),'0100')
    line = line.replace(chr(0b0010),'0010')
    line = line.replace(chr(0b0001),'0001')
    line = line.replace(chr(0b1010),'n')
    sequence += line
#outputVerify = open('outputVerify.txt','wb')
#outputVerify.write(sequence)
#outputVerify.close()
print sequence
testBin.close()

#Shows the data of the binary file. Note that byte 6 is the newline character 0b1010.
testBin = open('fileA.txt.bin','rb')
list = ''
i=0
while True:
    b = testBin.read(1)
    i += 1
    if not b:
    break #due to eof
    list += b
    print 'byte: ' + str(i) + ' is '+ '{0:04b}'.format(ord(b)) +' and has decimal representation: ' + str(ord(b))
testBin.close()

Edit 2 (moving my comment to the answer body): If this isn’t for an assignment or to interface with someone’s software, I recommend encoding your nucleotides as 0b00, 0b01,0b10, and 0b11 to save time and space. You can still use the 4-bit 0b1010 newline character to separate nucleotide sequences.



Source: stackoverflow