i am a beginner and want to make a barcode out of this DNA sequence by using pyhton code. it s supposed to read each 1024 nucleotide and checks for mers (a combination of 4 nucleotides i.g. AAAA, AAAC, AAAG, AAAT ..... TTTT). each mer holds an index in an array (size = 256) if it found AAAA within the first 1024 it stores its count in it s index and so on, then to the next 1024 until it s done with the whole sequence. that will create a 2D array which will be turned into a png in gray scale.

my problem is that it took only the first 1024 and displayed it on the entire 1024X256 image.

DNA: https://1drv.ms/f/s!AuXxv7yqjA_FlS_ujYOMUvikWg8E

#read the DNA sequence
fasta_file = open(r C:pathEscherichia_coli_ATCC_10798.fasta , r )
SE =fasta_file.read()
fasta_file.close()
seq = SE[177:]
dna_sequence = seq.replace("
","")

# Sample size and mer length
#sample is the window that will go thorugh the whole sequance
sample_size = 1024
mer_length = 4

# Array to store the counts of each mer
barcode = [0] * 256

# Generate all possible 4-mers
mers = []
for i in range(256):
    mer = ""
    for j in range(4):
        mer += "ACGT"[i % 4]
        i //= 4
    mers.append(mer)


# Loop through the sample and count the occurrences of each mer
for w in range(sample_size):
    mer = dna_sequence[w:w+mer_length]
    barcode[mers.index(mer)] += 2

# Print the counts of each mer
    #print(mers[i], ":", barcode[i])
print(barcode)



# image
    # Python program to convert numpy array to image
    # import pillow library
from PIL import Image
import numpy as np

    # define a main function
    # Create the barcode array with the same shape as the desired image
code = np.array(barcode, dtype=np.uint8)

    # Create an Image object from the barcode array
image = Image.fromarray(code)

    # Reshape the image to the desired size (1024x4000)
image = image.resize((1024, 4000))

    # Save the image
image.save( Escherichia_coli.png )

    # Display the image (optional)
image.show()

the dark image is what i got the other one is what i was supposed to getenter image description here my output

i don t know how to attach the DNA sequence. some info: genome_id="531534bd23a542ae" atcc_catalog_number="ATCC 10798" species="Escherichia coli"

link to similar genome:

https://www.ncbi.nlm.nih.gov/assembly/GCA_028644645.1