def main(): # Parse command line arguments options, args = doc_optparse.parse( __doc__ ) try: lnorm = bool( options.lnorm ) recalculate = bool( options.recalculate ) except: doc_optparse.exit() hox70 = score.build_scoring_scheme( """ A C G T 91 -114 -31 -123 -114 100 -125 -31 -31 -125 100 -114 -123 -31 -114 91 """, 400, 30, default=0 ) maf_reader = maf.Reader( sys.stdin ) for m in maf_reader: if m.text_size == 0: print "NA" continue s = m.score # Recalculate? if recalculate: s = hox70.score_alignment( m ) # Normalize? if lnorm: s = s / m.text_size # Print print s
def main(): # Parse command line arguments options, args = doc_optparse.parse(__doc__) try: lnorm = bool(options.lnorm) recalculate = bool(options.recalculate) except Exception: doc_optparse.exit() hox70 = score.build_scoring_scheme(""" A C G T 91 -114 -31 -123 -114 100 -125 -31 -31 -125 100 -114 -123 -31 -114 91 """, 400, 30, default=0) maf_reader = maf.Reader(sys.stdin) for m in maf_reader: if m.text_size == 0: print("NA") continue s = m.score # Recalculate? if recalculate: s = hox70.score_alignment(m) # Normalize? if lnorm: s = s / m.text_size # Print print(s)