def _read_sumstats(args, log, fh, alleles=False, dropna=False): '''Parse summary statistics.''' log.log('Reading summary statistics from {S} ...'.format(S=fh)) if args.snplist: log.log( 'and extracting SNPs specified in {S} ...'.format(S=args.snplist)) sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna, slh=args.snplist) else: sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna) log_msg = 'Read summary statistics for {N} SNPs.' log.log(log_msg.format(N=len(sumstats))) m = len(sumstats) sumstats = sumstats.drop_duplicates(subset='SNP') if m > len(sumstats): log.log('Dropped {M} SNPs with duplicated rs numbers.'.format( M=m - len(sumstats))) return sumstats
def _read_sumstats(args, log, fh, alleles=False, dropna=False): # Parse summary statistics. log.log('Reading summary statistics from {S} ...'.format(S=fh)) sumstats, n_codings = ps.sumstats(fh, args.additive, args.dominance, args.gxe, alleles=alleles, dropna=dropna) log_msg = 'Read summary statistics for {N} SNPs.' log.log(log_msg.format(N=len(sumstats))) m = len(sumstats) sumstats = sumstats.drop_duplicates(subset='SNP') if m > len(sumstats): log.log('Dropped {M} SNPs with duplicated rs numbers.'.format(M=m - len(sumstats))) return sumstats, n_codings
def _read_sumstats(args, log, fh, alleles=False, dropna=False): '''Parse summary statistics.''' log.log('Reading summary statistics from {S} ...'.format(S=fh)) sumstats = ps.sumstats(fh, alleles=alleles, dropna=dropna) log_msg = 'Read summary statistics for {N} SNPs.' log.log(log_msg.format(N=len(sumstats))) m = len(sumstats) sumstats = sumstats.drop_duplicates(subset='SNP') if m > len(sumstats): log.log( 'Dropped {M} SNPs with duplicated rs numbers.'.format(M=m - len(sumstats))) return sumstats