INNER CODE UNIT · Python

peddy

brentp/peddy · peddy/cli.py:151

def peddy(vcf, ped, plot, procs, prefix, each, sites, loglevel):
    """pleasingly pythonic pedigree manipulation"""
    coloredlogs.install(log_level=loglevel)
    log.info("Running Peddy version %s", __version__)
    prefix = prefix or vcf[:-6]

    if sites == "hg38":
        sites = op.join(op.dirname(__file__), 'GRCH38.sites')

    tmpl = string.Template(open(op.join(op.dirname(__file__), "tmpl.html")).read())

    ped_obj = Ped(ped)
    prefix = prefix.rstrip(".-")

    samples = VCF(vcf).samples

    ped_df = pd.read_csv(ped,
                           header=None,

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