#!/opt/chipster/tools/Python-2.7.12/bin/python """ Read a MAF from standard input and determine the mean length of ungapped pieces 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 ): 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()