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()
