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 = []