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#!/usr/bin/python3
"""
Translate a maf file containing gap ambiguity characters as produced by
'maf_tile_2.py' to a new file in which "#" (contiguous) is replaced by "-" and
all other types are replaces by "*".
TODO: This could be much more general, should just take the translation table
from the command line.
usage: %prog < maf > maf
"""
import sys
from bx.align import maf
table = str.maketrans("#=X@", "-***")
def main():
maf_reader = maf.Reader(sys.stdin)
maf_writer = maf.Writer(sys.stdout)
for m in maf_reader:
for c in m.components:
c.text = c.text.translate(table)
maf_writer.write(m)
maf_writer.close()
if __name__ == "__main__":
main()
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