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#!/usr/bin/python3
"""
Read a feature file containing a 0 or 1 on each line, output
all mafs whose index in maf_file corresponds to a row having a 1
usage: %prog feature_file < maf_file
"""
import sys
import bx.align.maf
def __main__():
feature_file = sys.argv[1]
if len(sys.argv) > 2:
match = int(sys.argv[2])
else:
match = 1
feature_vector = [int(line) for line in open(feature_file)]
maf_reader = bx.align.maf.Reader(sys.stdin, parse_e_rows=True)
maf_writer = bx.align.maf.Writer(sys.stdout)
index = 0
for m in maf_reader:
if feature_vector[index] == match:
maf_writer.write(m)
index += 1
if __name__ == "__main__":
__main__()
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