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How to use the pyfaidx.bed_split function in pyfaidx

To help you get started, we’ve selected a few pyfaidx examples, based on popular ways it is used in public projects.

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mdshw5 / pyfaidx / pyfaidx / bedmask.py View on Github

def mask_sequence(args):
    assert len(args.default_seq) == 1
    fasta = Fasta(args.fasta, mutable=True)
    for line in args.bed:
        rname, start, end = bed_split(line)
        if args.action == 'replace':
            fasta[rname][start:end] = (end - start) * args.default_seq
        elif args.action == 'lowercase':
            fasta[rname][start:end] = fasta[rname][start:end].lowercase()

mdshw5 / pyfaidx / pyfaidx / cli.py View on Github

def split_regions(args):
    if args.bed:
        regions_to_fetch = args.bed
        split_function = bed_split
    else:
        regions_to_fetch = args.regions
        split_function = ucsc_split
    return (regions_to_fetch, split_function)