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#!/usr/bin/python3
"""
Pass through blocks from a maf file until a certain number of columns
have been passed.
usage: %prog -c cols < maf > maf
"""
import sys
from optparse import OptionParser
from bx.align import maf
def __main__():
parser = OptionParser()
parser.add_option("-c", "--cols", action="store")
(options, args) = parser.parse_args()
maf_reader = maf.Reader(sys.stdin, parse_e_rows=True)
maf_writer = maf.Writer(sys.stdout)
if not options.cols:
raise Exception("Cols argument is required")
cols = int(options.cols)
count = 0
for m in maf_reader:
maf_writer.write(m)
count += m.text_size
if count >= cols:
return
if __name__ == "__main__":
__main__()
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