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#!/usr/bin/python3
"""
Read a PAIRWISE maf from stdin and print the percent identity of each
alignment, where percent identity is defined as the number of matching columns
over the number of aligned (non-gap) columns.
TODO: Generalize for more than two species
usage: %prog < maf > out
"""
import sys
from bx.align import maf
def __main__():
maf_reader = maf.Reader(sys.stdin)
for m in maf_reader:
match = 0
total = 0
for i in range(0, m.text_size):
a = m.components[0].text[i].lower()
b = m.components[1].text[i].lower()
if a == "-" or b == "-":
continue
elif a == b:
match += 1
total += 1
print(match / total)
if __name__ == "__main__":
__main__()
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