def recode(self, out=None):
if out is None:
self.out_prefix = temp_file()
else:
self.out_prefix = out
self.result = self.out_prefix + ".recode.vcf"
self.cmd = self.cmd.bake("--recode")
return self.execute()
def inner_join(a, b, out=None): a_snps = open(a.write_snplist().snplist()).readlines() b_snps = open(b.write_snplist().snplist()).readlines() union_snps = temp_file() o = open(union_snps, "w") u = list(set(a_snps) & set(b_snps)) for s in u: o.write(s) o.close() a_reduced = PlinkData(a.filename).extract(union_snps).make_bed() b_reduced = PlinkData(b.filename).extract(union_snps).make_bed() return a_reduced.bmerge(b_reduced, out)
def snps_only(self, out=None):
if out is None: out = temp_file() + ".vcf.gz"
o = gzip.GzipFile(out, "w")
bases = ["A", "T", "G", "C", "a", "t", "g", "c"]
header = None
for line in self.f:
if re.search("##", line):
o.write(line)
elif re.search("#", line):
o.write(line)
header = re.split("\t", line)
else:
info = re.split("\t", line)
if info[header.index("REF")] in bases:
if info[header.index("ALT")] in bases:
o.write(line)
o.close()
return VCFData(out)
def reset_ids(self, out=None):
if out is None: out = temp_file() + ".vcf.gz"
o = gzip.GzipFile(out, "w")
header = None
for line in self.f:
if re.search("##", line):
o.write(line)
elif re.search("#", line):
o.write(line)
header = re.split("\t", line)
else:
info = re.split("\t", line)
new_id = (info[header.index("#CHROM")],
info[header.index("POS")],
info[header.index("REF")],
info[header.index("ALT")])
info[header.index("ID")] = "%s_%s_%s_%s" % new_id
o.write("\t".join(info))
o.close()
return VCFData(out)
def execute(self, out=None):
if out is None: out = temp_file()
self.cmd("--out", out)
return PlinkData(out)
