def run(args):
col_num = get_col_num(args.c)
file_iter = (l.rstrip("\r\n").split("\t")
for l in open(args.file) if l[0] != "#")
pvals = np.array([float(b[col_num]) for b in file_iter])
kwargs = {"bins": args.n} if args.n else {}
hist, bins = np.histogram(pvals, normed=True, **kwargs)
xlabels = "|".join("%.2f-%.2f" % b for b in pairwise(bins))
print "#", chart(hist, xlabels)
hist, bins = np.histogram(pvals, normed=False, **kwargs)
print "# median: %.3f mean:%.3f; std: %.3f min:%.3f; max:%.3f" % (
np.median(pvals), pvals.mean(), pvals.std(), pvals.min(), pvals.max())
try:
from scipy.stats import chisquare
chisq, p = chisquare(hist)
print "#chi-square test of uniformity. p: %.3g " \
"(low value means reject null of uniformity)" % p
except ImportError:
pass
print "#bin_start\tbin_end\tn"
for bin, val in zip(pairwise(bins), hist):
print "%.2f\t%.2f\t%i" % (bin[0], bin[1], val)
def create_acf_list(lags):
acfs = []
for lag_min, lag_max in pairwise(lags):
acfs.append((lag_min, lag_max,
# array uses less memory than list.
{"x": array("f"), "y": array("f")}))
acfs.reverse()
return acfs
def create_acf_list(lags):
acfs = []
for lag_min, lag_max in pairwise(lags):
acfs.append((lag_min, lag_max,
# array uses less memory than list.
{"x": array("f"), "y": array("f")}))
acfs.reverse()
return acfs
def run(args):
col_num = get_col_num(args.c)
file_iter = (l.rstrip("\r\n").split("\t")
for l in ts.nopen(args.file) if l[0] != "#")
pvals = np.array([float(b[col_num]) for b in file_iter])
kwargs = {"bins": args.n} if args.n else {}
hist, bins = np.histogram(pvals, normed=True, **kwargs)
xlabels = "|".join("%.2f-%.2f" % b for b in pairwise(bins))
hist, bins = np.histogram(pvals, normed=False, **kwargs)
print("# median: %.3f mean:%.3f; std: %.3f min:%.3f; max:%.3f" % (
np.median(pvals), pvals.mean(), pvals.std(), pvals.min(), pvals.max()))
try:
from scipy.stats import chisquare
chisq, p = chisquare(hist)
print("#chi-square test of uniformity. p: %.3g " \
"(low value means reject null of uniformity)" % p)
except ImportError:
pass
print("#bin_start\tbin_end\tn")
for bin, val in zip(pairwise(bins), hist):
print("%.2f\t%.2f\t%i" % (bin[0], bin[1], val))