pybigwig

import pyBigWig import os # Define a temporary bigWig file name temp_bw_file = "temp_quickstart.bigWig" # --- Writing a new bigWig file for demonstration --- # Chromosome sizes are required for writing chrom_sizes = {"chr1": 100000, "chr2": 50000} bw_write = pyBigWig.open(temp_bw_file, "w") bw_write.addHeader([(name, size) for name, size in chrom_sizes.items()]) # Add some dummy entries bw_write.addEntries( ["chr1"] * 5, [0, 100, 200, 300, 400], [99, 199, 299, 399, 499], [0.1, 0.2, 0.3, 0.4, 0.5] ) bw_write.addEntries("chr1", 5000, 5010, [1.0]*10, step=1, span=1) bw_write.addEntries("chr2", 1000, 1005, [2.0]*5, step=1, span=1) bw_write.close() print(f"Created dummy bigWig file: {temp_bw_file}\n") # --- Reading from the bigWig file --- bw = pyBigWig.open(temp_bw_file) print(f"Chromosomes found: {bw.chroms()}\n") # Get values from a specific region on chr1 values_chr1 = bw.values("chr1", 0, 500) print(f"Values on chr1 (0-500, first 10): {values_chr1[:10]}...\n") # Get summary statistics for a region summary_chr1 = bw.stats("chr1", 0, 1000, type="mean") print(f"Mean value on chr1 (0-1000): {summary_chr1[0]}\n") # Get intervals (start, end, value) for a region intervals_chr1 = bw.intervals("chr1", 0, 1000) print(f"Intervals on chr1 (0-1000, first 3): {intervals_chr1[:3]}...\n") # Close the bigWig file to release resources bw.close() # Clean up the temporary file if os.path.exists(temp_bw_file): os.remove(temp_bw_file) print(f"Cleaned up temporary file: {temp_bw_file}")