python VCF file 정보 추출 (chromosome) 하고 plot 만들기

python VCF file 정보 추출 (chromosome) 하고 plot 만들기

 

import matplotlib.pyplot as plt

def extract_chromosome(vcf_file):
    chromosomes = []
    with open(vcf_file, 'r') as f:
        for line in f:
            # Skip header lines
            if line.startswith('#'):
                continue
            # Split the line into fields
            fields = line.strip().split('\t')
            # Extract chromosome information
            chromosome = fields[0]
            # Append the chromosome information to the list
            chromosomes.append(chromosome)
    return chromosomes

# Function to create a bar plot of chromosome frequencies
def plot_chromosome_frequencies(chromosomes):
    chromosome_counts = {chromosome: chromosomes.count(chromosome) for chromosome in set(chromosomes)}
    sorted_chromosomes = sorted(chromosome_counts.items(), key=lambda x: x[1], reverse=True)
    chromosome_names, counts = zip(*sorted_chromosomes)
    
    # Create bar plot
    plt.figure(figsize=(10, 6))
    plt.bar(chromosome_names, counts, color='skyblue')
    plt.xlabel('Chromosome')
    plt.ylabel('Frequency')
    plt.title('Chromosome Frequencies in VCF File')
    plt.xticks(rotation=45, ha='right')
    plt.tight_layout()
    plt.show()

# usage
if __name__ == "__main__":
    vcf_file = 'sample.vcf'
    chromosomes = extract_chromosome(vcf_file)
    plot_chromosome_frequencies(chromosomes)