)
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)))
