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#!/usr/bin/python3
"""
Read a MAF from standard input and determine the mean length of ungapped pieces
in each block.
usage: %prog < maf > out
"""
import sys
import bx.align.maf
def main():
for m in bx.align.maf.Reader(sys.stdin):
ungapped_columns = 0
ungapped_runs = 0
in_ungapped = False
for col in m.column_iter():
is_gap = "-" in col
if not is_gap:
ungapped_columns += 1
if in_ungapped and is_gap:
ungapped_runs += 1
in_ungapped = not is_gap
if in_ungapped:
ungapped_runs += 1
print(ungapped_columns / ungapped_runs)
if __name__ == "__main__":
main()
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