) args.frqfile = None args.frqfile_chr = None if args.overlap_annot and not args.not_M_5_50: if not ((args.frqfile and args.ref_ld) or (args.frqfile_chr and args.ref_ld_chr)): raise ValueError( 'Must set either --frqfile and --ref-ld or --frqfile-chr and --ref-ld-chr' ) if args.rg: sumstats.estimate_rg(args, log) elif args.h2: sumstats.estimate_h2(args, log) elif args.h2_cts: sumstats.cell_type_specific(args, log) # bad flags else: print header print 'Error: no analysis selected.' print 'ldsc.py -h describes options.' except Exception: ex_type, ex, tb = sys.exc_info() log.log(traceback.format_exc(ex)) raise finally: log.log('Analysis finished at {T}'.format(T=time.ctime())) time_elapsed = round(time.time() - start_time, 2) log.log('Total time elapsed: {T}'.format(T=sec_to_str(time_elapsed)))
if not args.overlap_annot or args.not_M_5_50: if args.frqfile is not None or args.frqfile_chr is not None: log.log('The frequency file is unnecessary and is being ignored.') args.frqfile = None args.frqfile_chr = None if args.overlap_annot and not args.not_M_5_50: if not ((args.frqfile and args.ref_ld) or (args.frqfile_chr and args.ref_ld_chr)): raise ValueError('Must set either --frqfile and --ref-ld or --frqfile-chr and --ref-ld-chr') if args.rg: sumstats.estimate_rg(args, log) elif args.h2: sumstats.estimate_h2(args, log) elif args.h2_cts: sumstats.cell_type_specific(args, log) # bad flags else: print header print 'Error: no analysis selected.' print 'ldsc.py -h describes options.' except Exception: ex_type, ex, tb = sys.exc_info() log.log( traceback.format_exc(ex) ) raise finally: log.log('Analysis finished at {T}'.format(T=time.ctime()) ) time_elapsed = round(time.time()-start_time,2) log.log('Total time elapsed: {T}'.format(T=sec_to_str(time_elapsed)))