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import sys
import gzip
import collections
def xopen(f):
return (gzip.open if f.endswith(".gz") else open)(f)
sites = collections.OrderedDict()
files = sys.argv[1:]
def key(toks):
return (toks[0], toks[1], toks[3], toks[4])
def anynonref(gts):
return any(gt.startswith(("0/1", "1/1")) for gt in gts)
header = []
for f in files:
header = []
for toks in (l.rstrip().split("\t") for l in xopen(f)):
if toks[0][0] == "#":
if toks[0] == "#CHROM":
toks = toks[:8]
header.append("\t".join(toks))
continue
if anynonref(toks[9:]):
sites[key(toks)] = "\t".join(toks[:8])
print("\n".join(header))
for k, line in sites.items():
print(line)
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