parser = ArgumentParser()
parser.add_argument("-p", "--selected_frags_path", required=True, type=str, help="")
parser.add_argument("-c", "--clustering_results", required=True, type=str, help="")
args = parser.parse_args()
# fragidx file
fragidx_pickle = args.selected_frags_path + "/index_Dict.pickle"
assert os.path.exists( fragidx_pickle )
frag_idx1 = open( "frags.idx1", "w" )
dict = pickle.load( open( fragidx_pickle, "rb" ) )[1]
for idx in dict.keys():
frag_idx1.write("%s %s %s %s %s\n" %( idx, dict[idx][0], dict[idx][1], dict[idx][2], dict[idx][3] ))
frag_idx1.close()
# get density_score_Dict.pickle"
scoretable = ScoreTable( args.selected_frags_path )
scoretable.density_score_reader( args.clustering_results )
# output all_density_rmsd.idx1
den_idx1 = open( "all_density_rmsd.idx1", "w" )
dict = pickle.load( open( "density_score_Dict.pickle", "rb" ) )
for pos in dict.keys():
for idx in dict[pos]:
if idx < 0: continue
den_idx1.write("%s %s %s\n" %( idx, dict[pos][idx][0], dict[pos][idx][1] ))
14: 0.0416,
15: 0.0422 }
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="")
parser.add_argument("-w", "--closab_weight", action="store_true", default=False, help="when it says it's closable, reweight it")
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 )
#!/usr/local/bin/python2.7
from argparse import ArgumentParser
from ScoreTable import ScoreTable
from sys import stderr, exit, stdout
if __name__=='__main__':
parser = ArgumentParser()
parser.add_argument("-p", "--selected_frags_path", type=str, help="")
parser.add_argument("-d", "--density_scorefile", type=str, help="")
parser.add_argument("-o", "--overlap_scorefile", type=str, help="")
parser.add_argument("-l", "--nonoverlap_scorefile", type=str, help="")
args = parser.parse_args()
scoretable = ScoreTable( args.selected_frags_path )
scoretable.score_files_reader( args.density_scorefile, args.overlap_scorefile, args.nonoverlap_scorefile )
#!/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()
#!/usr/local/bin/python2.7
from argparse import ArgumentParser
from ScoreTable import ScoreTable
from sys import stderr, exit, stdout
if __name__=='__main__':
'''
converting indexed scorefiles into npy
'''
parser = ArgumentParser()
parser.add_argument("-p", "--selected_frags_path", required=True, type=str, help="")
parser.add_argument("-d", "--density_scorefile", type=str, help="")
parser.add_argument("-o", "--overlap_scorefile", type=str, help="")
parser.add_argument("-l", "--nonoverlap_scorefile", type=str, help="")
args = parser.parse_args()
if not args.density_scorefile and not args.overlap_scorefile and not args.nonoverlap_scorefile:
stderr.write("ERROR: you need to at least specify one type of scorefile\n"); exit()
scoretable = ScoreTable( args.selected_frags_path )
if args.density_scorefile:
scoretable.density_score_reader( args.density_scorefile )
if args.overlap_scorefile:
scoretable.overlap_score_reader( args.overlap_scorefile )
if args.nonoverlap_scorefile:
scoretable.nonoverlap_score_reader( args.nonoverlap_scorefile )
