def calc_stats_total(af_lst, callable_sites): segs = len(af_lst) theta_w = pg.thetaW(n, segs) theta_w_site = theta_w / callable_sites pi = pg.pi_tajima(n, af_lst) pi_site = pi / callable_sites tajd = pg.TajimasD(n, segs, theta_w, pi) if tajd is None: tajd = 'NA' return callable_sites, segs, theta_w_site, pi_site, tajd
def calc_stats_region(pop, chrom, feature_id, feature_type, af_lst, callable_sites, out): segs = len(af_lst) theta_w = pg.thetaW(n, segs) theta_w_site = theta_w / callable_sites pi = pg.pi_tajima(n, af_lst) pi_site = pi / callable_sites tajd = pg.TajimasD(n, segs, theta_w, pi) if tajd is None: tajd = 'NA' print(pop, chrom, feature_id, feature_type, callable_sites, segs, theta_w_site, pi_site, tajd, sep='\t', file=out)
def calc_stats_chr(pop, af_lst, chrom, callable_file, out): callable_sites = count_callable(callable_file, chrom) segs = len(af_lst) theta_w = pg.thetaW(n, segs) theta_w_site = theta_w / callable_sites[1] pi = pg.pi_tajima(n, af_lst) pi_site = pi / callable_sites[1] tajd = pg.TajimasD(n, segs, theta_w, pi) if tajd is None: tajd = 'NA' print(pop, chrom, callable_sites[0], callable_sites[1], segs, theta_w_site, pi_site, tajd, sep='\t', file=out) return callable_sites[0], callable_sites[1]
sites = calc_stats_chr(args.pop_id, af, c, args.callable, outfile) total_sites += sites[0] total_callable += sites[1] del af[:] if args.sfs: for c in total_ac: sfs[min(n - c, c)] += 1 sfs[0] += (total_callable - len(total_ac)) S = len(total_af) thetaw = pg.thetaW(n, S) thetaw_site = thetaw / total_callable pi_taj = pg.pi_tajima(n, total_af) pisite = pi_taj / total_callable taj_d = pg.TajimasD(n, S, thetaw, pi_taj) print(args.pop_id, 'Total', total_sites, total_callable, S, thetaw_site, pisite, taj_d, sep='\t', file=outfile) if args.bed: compressed = False bed_dict = {} wwss_alleles = [('A', 'T'), ('T', 'A'), ('C', 'G'), ('G', 'C')] ac_dict = {} af_dict = {} sites_dict = {} ac_list = []