WAP to plot codon frequency in a given sequence

Sure, here is a simple Python script using Biopython and matplotlib to plot codon frequency in a given sequence:

from Bio import SeqIO
from Bio.SeqUtils import CodonUsage
import matplotlib.pyplot as plt

# Read the sequence
sequence = SeqIO.read("sequence.fasta", "fasta")

# Create a CodonUsage object
codon_usage = CodonUsage.CodonsDict

# Count codon usage in the sequence
for i in range(0, len(sequence.seq), 3):
    codon = sequence.seq[i:i+3]
    if codon in codon_usage:
        codon_usage[codon] += 1

# Plot codon frequency
plt.bar(codon_usage.keys(), codon_usage.values())
plt.show()

This script reads a sequence from a fasta file, counts the usage of each codon in the sequence, and plots the frequency of each codon.

Please replace "sequence.fasta" with your actual fasta file. Also, this script assumes that the sequence is divisible by 3. If it's not, you might want to add some error checking code to handle the last 1 or 2 bases.

Note: You need to have Biopython and matplotlib installed in your Python environment to run this script. You can install them using pip:

pip install biopython matplotlib