INNER CODE UNIT · Python

out

brentp/peddy · peddy/king.py:16

        out = out[:-3]
    if out.endswith(".vcf"): out = out[:-4]

    elog = open(out + ".plink.err", "w")
    olog = open(out + ".plink.log", "w")
    subprocess.check_call([plink, "--vcf", vcf_path, "--make-bed",
                           "--noweb",
                           "--out", out, "--biallelic-only", "--geno",
                           "0.95", "--vcf-half-call", "m"], stderr=elog,
                           stdout=olog)
    elog.close() and olog.close()

    elog = open(out + ".plink.err", "w")
    olog = open(out + ".plink.log", "w")
    subprocess.check_call([king, "-b", out + ".bed", "--kinship",
                           "--prefix", out], stderr=elog, stdout=olog)
    elog.close() and olog.close()

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