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#!/usr/bin/env python
# Author: Lenna X. Peterson
# github.com/lennax
# arklenna at gmail dot com
import argparse
import logging
from vcf import SampleFilter
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("file", help="VCF file to filter")
parser.add_argument("-o", metavar="outfile",
help="File to write out filtered samples")
parser.add_argument("-f", metavar="filters",
help="Comma-separated list of sample indices or names \
to filter")
parser.add_argument("-i", "--invert", action="store_true",
help="Keep rather than discard the filtered samples")
parser.add_argument("-q", "--quiet", action="store_true",
help="Less output")
args = parser.parse_args()
if args.quiet:
log_level = logging.WARNING
else:
log_level = logging.INFO
logging.basicConfig(format='%(message)s', level=log_level)
sf = SampleFilter(infile=args.file, outfile=args.o,
filters=args.f, invert=args.invert)
if args.f is None:
print("Samples:")
for idx, val in enumerate(sf.samples):
print("{0}: {1}".format(idx, val))
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