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 )