Neel
Bioinformatics Beginner
Our Sponsors
Python script to split a genome sequence into overlapping windows of 100 base pairs
By Neel 13 days ago
def split_genome(sequence, window_size=100, step=1):
"""
Splits a genome sequence into overlapping windows.
Args:
sequence (str): The genome sequence.
window_size (int): Size of each window (default: 100).
step (int): Step size for overlapping (default: 1).
Returns:
list: A list of genome windows.
"""
windows = []
for i in range(0, len(sequence) - window_size + 1, step):
windows.append(sequence[i:i + window_size])
return windows
# Example usage:
if __name__ == "__main__":
genome_sequence = "ATGCGTACGTTAGCTACGATCGTACGATCGTACGATCGATCGTAGCATCGATCGTACG"
window_size = 100
step_size = 1
# Get overlapping windows
genome_windows = split_genome(genome_sequence, window_size, step_size)
# Print results
for idx, window in enumerate(genome_windows):
print(f"Window {idx + 1}: {window}")
