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#!/usr/bin/python3
"""
Filter maf blocks for presence of wildcard columns. Blocks must meet the
criteria of having at least `min_good` columns, each of which has more than
`min_species` rows that are NOT wildcard bases ('*').
TODO: Allow specifying the character of the wildcard base.
usage: %prog min_good min_species < maf > maf
"""
import sys
from bx.align import maf
def main():
min_good = int(sys.argv[1])
min_species = int(sys.argv[2])
maf_reader = maf.Reader(sys.stdin, parse_e_rows=True)
maf_writer = maf.Writer(sys.stdout)
for m in maf_reader:
good = 0
for col in m.column_iter():
if col.count("*") <= min_species:
good += 1
if good >= min_good:
maf_writer.write(m)
if __name__ == "__main__":
main()
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