parser.add_argument("-nw", "--nonclosab_weight", type=float, default=10, help="when it says not closable, reweight it") args = parser.parse_args() # try to find indexing file from the folder, if not, create one indexing = ScoreTable( args.selected_frags_path ) ## read scorefile if args.closab_weight: outfn = args.scorefile+".clean.weighted.idx" else: outfn = args.scorefile+".clean.idx" lines = "" if args.scoretype == "overlap": lines = indexing.raw_overlap_score_cleaner( args.scorefile ) elif args.scoretype == "nonoverlap": if args.closab_weight: lines = indexing.raw_nonoverlap_score_cleaner( args.scorefile, gap_weights_dict, args.nonclosab_weight ) else: lines = indexing.raw_nonoverlap_score_cleaner( args.scorefile ) if not lines: stderr.write("ERROR: nothing being done!\n"); exit() outfile = open( outfn, "w" ) outfile.write( lines ) outfile.close()
#!/usr/local/bin/python2.7 from argparse import ArgumentParser from ScoreTable import ScoreTable from sys import stderr, exit, stdout from os.path import basename if __name__=='__main__': parser = ArgumentParser() parser.add_argument("-p", "--selected_frags_path", required=True, help="") parser.add_argument("-s", "--scorefile", required=True, help="") parser.add_argument("-t", "--scoretype", required=True, choices=["overlap","nonoverlap"], help="") args = parser.parse_args() indexing = ScoreTable( args.selected_frags_path ) ## read scorefile outfile = open( args.scorefile+".clean.idx", "w" ) lines = "" if args.scoretype == "overlap": lines = indexing.raw_overlap_score_cleaner( args.scorefile ) elif args.scoretype == "nonoverlap": lines = indexing.raw_nonoverlap_score_cleaner( args.scorefile ) outfile.write( lines ) outfile.close()