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] ))
#!/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 )