def minimac(args):
"""
%prog batchminimac input.txt
Use MINIMAC3 to impute vcf on all chromosomes.
"""
p = OptionParser(minimac.__doc__)
p.set_home("shapeit")
p.set_home("minimac")
p.set_outfile()
p.set_chr()
p.set_ref()
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
txtfile, = args
ref = opts.ref
mm = MakeManager()
pf = txtfile.split(".")[0]
allrawvcf = []
alloutvcf = []
chrs = opts.chr.split(",")
for x in chrs:
px = CM[x]
chrvcf = pf + ".{0}.vcf".format(px)
if txtfile.endswith(".vcf"):
cmd = "vcftools --vcf {0} --chr {1}".format(txtfile, x)
cmd += " --out {0}.{1} --recode".format(pf, px)
cmd += " && mv {0}.{1}.recode.vcf {2}".format(pf, px, chrvcf)
else: # 23andme
cmd = "python -m jcvi.formats.vcf from23andme {0} {1}".format(txtfile, x)
cmd += " --ref {0}".format(ref)
mm.add(txtfile, chrvcf, cmd)
chrvcf_hg38 = pf + ".{0}.23andme.hg38.vcf".format(px)
minimac_liftover(mm, chrvcf, chrvcf_hg38, opts)
allrawvcf.append(chrvcf_hg38)
minimacvcf = "{0}.{1}.minimac.dose.vcf".format(pf, px)
if x == "X":
minimac_X(mm, x, chrvcf, opts)
elif x in ["Y", "MT"]:
cmd = "python -m jcvi.variation.impute passthrough"
cmd += " {0} {1}".format(chrvcf, minimacvcf)
mm.add(chrvcf, minimacvcf, cmd)
else:
minimac_autosome(mm, x, chrvcf, opts)
# keep the best line for multi-allelic markers
uniqvcf= "{0}.{1}.minimac.uniq.vcf".format(pf, px)
cmd = "python -m jcvi.formats.vcf uniq {0} > {1}".\
format(minimacvcf, uniqvcf)
mm.add(minimacvcf, uniqvcf, cmd)
minimacvcf_hg38 = "{0}.{1}.minimac.hg38.vcf".format(pf, px)
minimac_liftover(mm, uniqvcf, minimacvcf_hg38, opts)
alloutvcf.append(minimacvcf_hg38)
if len(allrawvcf) > 1:
rawhg38vcfgz = pf + ".all.23andme.hg38.vcf.gz"
cmd = "vcf-concat {0} | bgzip > {1}".format(" ".join(allrawvcf), rawhg38vcfgz)
mm.add(allrawvcf, rawhg38vcfgz, cmd)
if len(alloutvcf) > 1:
outhg38vcfgz = pf + ".all.minimac.hg38.vcf.gz"
cmd = "vcf-concat {0} | bgzip > {1}".format(" ".join(alloutvcf), outhg38vcfgz)
mm.add(alloutvcf, outhg38vcfgz, cmd)
mm.write()