bed_utils.py 文件源码

def subtract(bed1, bed2, bedOut):
    if not bed2:
        shutil.copyfile(bed1,bedOut)
        return

    with open(bed1) as f:
        bed_dict1 = tk_io.get_target_regions(f)

    with open(bed2) as f:
        bed_dict2 = tk_io.get_target_regions(f)

    bed_dict_subtract = {}
    for chrom in bed_dict1:
        if not chrom in bed_dict_subtract:
            bed_dict_subtract[chrom] = tk_regions.Regions([])
        for start, end in bed_dict1[chrom]:
            overlappings = []
            if chrom in bed_dict2:
                overlappings = bed_dict2[chrom].overlapping_regions(start, end)
            for interval in interval_subtract(start, end, overlappings):
                bed_dict_subtract[chrom].add_region(interval)

    writeOut(bed_dict_subtract, bedOut)