INNER CODE UNIT · Python

run

brentp/peddy · peddy/cli.py:28

def run(args):
    check, pedf, vcf, plot, prefix, each, ncpus, sites = args
    # only print warnings for het_check
    p = Ped(pedf, warn=False)
    log.info("\033[1;31m%s\033[0m" % check)

    t0 = time.time()
    sys.stdout.flush()
    background_df = None
    if plot:
        plot = prefix + "." + check + ".png"

    if check in ("ped_check", "het_check"):
        kwargs = {'sites': sites}
        df = getattr(p, check)(vcf, plot=plot, each=each, ncpus=ncpus,
                               prefix=prefix, **kwargs)
        if check == "het_check":
            df, background_df = df

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