#!/opt/chipster/tools/Python-2.7.12/bin/python """ Read a MAF from standard input and print the fraction of gap columns in each block. usage: %prog < maf > out """ from __future__ import division import sys import bx.align.maf def main(): for m in bx.align.maf.Reader( sys.stdin ): gaps = 0 for col in m.column_iter(): if ( '-' in col ): gaps += 1 print gaps / m.text_size if __name__ == "__main__": main()