generate random genome position given chromosome_size.tsv

random_genomic_position.py

#!python3
import click
import random


def read_chrom_size(chrom_size):
    chrom_size_dict = {}
    with open(chrom_size) as f:
        for line in f:
            line = line.strip().split()
            chrom_size_dict[line[0]] = int(line[1])
    return chrom_size_dict


@click.command()
@click.option("--chrom-size", "-cs", default=None, help="Chromosome size file")
def main(chrom_size):
    """
    first read chromosome size
    then generate random chromosome position with possibilities adjusted to
    chromosome length
    then use click.echo to print it
    """
    chrom_size_dict = read_chrom_size(chrom_size)
    # random.seed(42)
    which_chr = random.choices(
        list(chrom_size_dict.keys()), weights=list(chrom_size_dict.values())
    )
    which_pos = random.randint(1, chrom_size_dict[which_chr[0]] + 1)
    click.echo("{}:{}".format(which_chr[0], which_pos))


if __name__ == "__main__":
    main()