def compilevcf(args):
"""
%prog compilevcf dir
Compile vcf outputs into lists.
"""
from jcvi.variation.str import LobSTRvcf
p = OptionParser(compilevcf.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
folder, = args
vcf_files = iglob(folder, "*.vcf,*.vcf.gz")
for vcf_file in vcf_files:
try:
p = LobSTRvcf(columnidsfile=None)
p.parse(vcf_file, filtered=False)
res = p.items()
if res:
k, v = res[0]
res = v.replace(',', '/')
else:
res = "-1/-1"
num = op.basename(vcf_file).split(".")[0]
print num, res
except (TypeError, AttributeError) as e:
p = TREDPARSEvcf(vcf_file)
continue
