def acf(fnames, lags, col_num0, partial=True, simple=False, mlog=True):
"""
calculate the correlation of the numbers in `col_num0` from the bed files
in `fnames` at various lags. The lags are specified by distance. Partial
autocorrelation may be calculated as well.
Since the bed files may be very large, this attempts to be as memory
efficient as possible while still being very fast for a pure python
implementation.
"""
# reversing allows optimization below.
from multiprocessing import set_start_method
set_start_method("fork", force=True)
imap = get_map()
arg_list = [] # chaining
for fname in fnames:
# groupby chromosome.
arg_list = chain(arg_list, ((list(chromlist), lags) for chrom, \
chromlist in \
groupby(bediter(fname, col_num0), lambda a: a["chrom"])))
unmerged_acfs = [] # separated by chrom. need to merge later.
for chrom_acf in imap(_acf_by_chrom, arg_list):
unmerged_acfs.append(chrom_acf)
acfs = merge_acfs(unmerged_acfs)
acf_res = {}
xs = np.array([], dtype='f')
ys = np.array([], dtype='f')
# iterate over it backwards and remove to reduce memory.
while len(acfs):
lmin, lmax, xys = acfs.pop()
if partial:
xs, ys = np.array(xys["x"]), np.array(xys["y"])
else:
# add the inner layers as we move out.
xs = np.hstack((xs, xys["x"]))
ys = np.hstack((ys, xys["y"]))
if len(xs) == 0:
print("no values found at lag: %i-%i. skipping" \
% (lmin, lmax), file=sys.stderr)
continue
if mlog:
xs[xs == 0] = 1e-12
ys[ys == 0] = 1e-12
xs, ys = -np.log10(xs), -np.log10(ys)
#slope, intercept, corr, p_val, stderr = ss.linregress(xs, ys)
# NOTE: using pearson correlation, which assumes normality.
# could switch to spearman as below.
corr, p_val = ss.spearmanr(xs, ys)
if simple:
acf_res[(lmin, lmax)] = corr
else:
acf_res[(lmin, lmax)] = (corr, len(xs), p_val)
return sorted(acf_res.items())
def acf(fnames, lags, col_num0, partial=True, simple=False, mlog=True):
"""
calculate the correlation of the numbers in `col_num0` from the bed files
in `fnames` at various lags. The lags are specified by distance. Partial
autocorrelation may be calculated as well.
Since the bed files may be very large, this attempts to be as memory
efficient as possible while still being very fast for a pure python
implementation.
"""
# reversing allows optimization below.
imap = get_map()
arg_list = [] # chaining
for fname in fnames:
# groupby chromosome.
arg_list = chain(arg_list, ((list(chromlist), lags) for chrom, \
chromlist in \
groupby(bediter(fname, col_num0), lambda a: a["chrom"])))
unmerged_acfs = [] # separated by chrom. need to merge later.
for chrom_acf in imap(_acf_by_chrom, arg_list):
unmerged_acfs.append(chrom_acf)
acfs = merge_acfs(unmerged_acfs)
acf_res = {}
xs = np.array([], dtype='f')
ys = np.array([], dtype='f')
# iterate over it backwards and remove to reduce memory.
while len(acfs):
lmin, lmax, xys = acfs.pop()
if partial:
xs, ys = np.array(xys["x"]), np.array(xys["y"])
else:
# add the inner layers as we move out.
xs = np.hstack((xs, xys["x"]))
ys = np.hstack((ys, xys["y"]))
if len(xs) == 0:
print("no values found at lag: %i-%i. skipping" \
% (lmin, lmax), file=sys.stderr)
continue
if mlog:
xs[xs == 0] = 1e-12
ys[ys == 0] = 1e-12
xs, ys = -np.log10(xs), -np.log10(ys)
#slope, intercept, corr, p_val, stderr = ss.linregress(xs, ys)
# NOTE: using pearson correlation, which assumes normality.
# could switch to spearman as below.
corr, p_val = ss.spearmanr(xs, ys)
if simple:
acf_res[(lmin, lmax)] = corr
else:
acf_res[(lmin, lmax)] = (corr, len(xs), p_val)
return sorted(acf_res.items())
def pipeline(col_num, step, dist, acf_dist, prefix, threshold, seed,
bed_files, mlog=True, region_filter_p=1, region_filter_n=None,
genome_control=False, db=None, use_fdr=True):
sys.path.insert(0, op.join(op.dirname(__file__), ".."))
from cpv import acf, slk, fdr, peaks, region_p, stepsize, filter
from cpv._common import genome_control_adjust, genomic_control, bediter
import operator
if step is None:
step = min(acf_dist, stepsize.stepsize(bed_files, col_num))
print("calculated stepsize as: %i" % step, file=sys.stderr)
lags = list(range(1, acf_dist, step))
lags.append(lags[-1] + step)
prefix = prefix.rstrip(".")
putative_acf_vals = acf.acf(bed_files, lags, col_num, simple=False,
mlog=mlog)
acf_vals = []
# go out to max requested distance but stop once an autocorrelation
# < 0.05 is added.
for a in putative_acf_vals:
# a is ((lmin, lmax), (corr, N))
# this heuristic seems to work. stop just above the 0.08 correlation
# lag.
if a[1][0] < 0.04 and len(acf_vals) > 2: break
acf_vals.append(a)
if a[1][0] < 0.04 and len(acf_vals): break
# save the arguments that this was called with.
with open(prefix + ".args.txt", "w") as fh:
print(" ".join(sys.argv[1:]) + "\n", file=fh)
import datetime
print("date: %s" % datetime.datetime.today(), file=fh)
from .__init__ import __version__
print("version:", __version__, file=fh)
with open(prefix + ".acf.txt", "w") as fh:
acf_vals = acf.write_acf(acf_vals, fh)
print("wrote: %s" % fh.name, file=fh)
print("ACF:\n", open(prefix + ".acf.txt").read(), file=sys.stderr)
spvals, opvals = array.array('f'), array.array('f')
with ts.nopen(prefix + ".slk.bed.gz", "w") as fhslk:
fhslk.write('#chrom\tstart\tend\tp\tregion-p\n')
for chrom, results in slk.adjust_pvals(bed_files, col_num, acf_vals):
fmt = chrom + "\t%i\t%i\t%.4g\t%.4g\n"
for row in results:
row = tuple(row)
fhslk.write(fmt % row)
opvals.append(row[-2])
spvals.append(row[-1])
print("# original lambda: %.2f" % genomic_control(opvals), file=sys.stderr)
del opvals
gc_lambda = genomic_control(spvals)
print("wrote: %s with lambda: %.2f" % (fhslk.name, gc_lambda),
file=sys.stderr)
if genome_control:
fhslk = ts.nopen(prefix + ".slk.gc.bed.gz", "w")
adj = genome_control_adjust([d['p'] for d in bediter(prefix + ".slk.bed.gz", -1)])
for i, line in enumerate(ts.nopen(prefix + ".slk.bed.gz")):
print("%s\t%.5g" % (line.rstrip("\r\n"), adj[i]), file=fhslk)
fhslk.close()
print("wrote: %s" % fhslk.name, file=sys.stderr)
with ts.nopen(prefix + ".fdr.bed.gz", "w") as fh:
fh.write('#chrom\tstart\tend\tp\tregion-p\tregion-q\n')
for bh, l in fdr.fdr(fhslk.name, -1):
fh.write("%s\t%.4g\n" % (l.rstrip("\r\n"), bh))
print("wrote: %s" % fh.name, file=sys.stderr)
fregions = prefix + ".regions.bed.gz"
with ts.nopen(fregions, "w") as fh:
list(peaks.peaks(prefix + ".fdr.bed.gz", -1 if use_fdr else -2, threshold, seed,
dist, fh, operator.le))
n_regions = sum(1 for _ in ts.nopen(fregions))
print("wrote: %s (%i regions)" % (fregions, n_regions), file=sys.stderr)
if n_regions == 0:
sys.exit()
with ts.nopen(prefix + ".regions-p.bed.gz", "w") as fh:
N = 0
fh.write("#chrom\tstart\tend\tmin_p\tn_probes\tz_p\tz_sidak_p\n")
# use -2 for original, uncorrected p-values in slk.bed
for region_line, slk_p, slk_sidak_p, sim_p in region_p.region_p(
prefix + ".slk.bed.gz",
prefix + ".regions.bed.gz", -2,
step):
fh.write("%s\t%.4g\t%.4g\n" % (region_line, slk_p, slk_sidak_p))
fh.flush()
N += int(slk_sidak_p < 0.05)
print("wrote: %s, (regions with corrected-p < 0.05: %i)" \
% (fh.name, N), file=sys.stderr)
regions_bed = fh.name
#if all(h in header for h in ('t', 'start', 'end')):
if region_filter_n is None: region_filter_n = 0
with ts.nopen(prefix + ".regions-t.bed", "w") as fh:
N = 0
for i, toks in enumerate(filter.filter(bed_files[0],
regions_bed, p_col_name=col_num)):
if i == 0: toks[0] = "#" + toks[0]
else:
if float(toks[6]) > region_filter_p: continue
if int(toks[4]) < region_filter_n: continue
#if region_filter_t and "/" in toks[7]:
# # t-pos/t-neg. if the lower one is > region_filter_t?
# vals = map(int, toks[7].split("/"))
# if min(vals) > region_filter_t: continue
N += 1
print("\t".join(toks), file=sys.stderr)
print(("wrote: %s, (regions with region-p "
"< %.3f and n-probes >= %i: %i)") \
% (fh.name, region_filter_p, region_filter_n, N),
file=sys.stderr)
try:
from cpv import manhattan
regions = manhattan.read_regions(fh.name)
manhattan.manhattan(prefix + ".slk.bed.gz", 3, prefix.rstrip(".") + ".manhattan.png",
False, ['#959899', '#484B4C'], "", False, None,
regions=regions, bonferonni=False)
except ImportError:
pass # they dont have matplotlib
if db is not None:
from cruzdb import Genome
g = Genome(db)
lastf = fh.name
with open(prefix + ".anno.%s.bed" % db, "w") as fh:
fh.write('#')
g.annotate(lastf, ("refGene", "cpgIslandExt"), out=fh,
feature_strand=True, parallel=len(spvals) > 500)
print("wrote: %s annotated with %s" % (fh.name, db), file=sys.stderr)
def manhattan(fname, col_num, image_path, no_log, colors, title, lines, ymax,
bonferonni=False, regions=None, subplots=False):
"""
regions is keyed by chromosome with [(start, stop), ...] extents of
the regions to highlight
"""
xs, ys, cs = [], [], []
region_xys = [] # highlight certain regions.
colors = cycle(colors)
chrom_centers = []
last_x = 0
nrows = 0
giter = [(seqid, list(rlist)) for seqid, rlist \
in groupby(bediter(fname, col_num), key=itemgetter('chrom'))]
region_xs, region_ys = [], []
new_bounds = []
rcolors = cycle(('#AE2117', '#EA352B'))
for seqid, rlist in sorted(giter, cmp=chr_cmp):
color = colors.next()
nrows += len(rlist)
# since chroms are on the same plot. add this chrom to the end of the
# last chrom
rcolor = rcolors.next()
region_xs = [last_x + r['start'] for r in rlist]
xs.extend(region_xs)
ys.extend([r['p'] for r in rlist])
cs.extend([color] * len(rlist))
if regions and seqid in regions:
regions_bounds = regions[seqid]
if len(regions_bounds) < 500:
region_xys.extend([(last_x + r['start'], r['p'], rcolor) for r in rlist \
if any((s - 1 <= r['start'] <= e + 1) for s, e in regions_bounds)])
else:
sys.stderr.write("regions for %s > 500, not plotting\n" % seqid)
# adjust the bounds of each region based on chrom.
new_bounds.extend([(last_x + s, last_x + e)
for s, e in regions_bounds])
# save the middle of the region to place the label
chrom_centers.append((seqid, (region_xs[0] + region_xs[-1]) / 2))
# keep track so that chrs don't overlap.
last_x = xs[-1]
xs = np.array(xs)
ys = np.array(ys) if no_log else -np.log10(ys)
plt.close()
f, ax = plt.subplots(1, figsize=(10, 6))
bonferonni_p = 0.05 / nrows
if title is not None:
plt.title(title)
ax.set_ylabel('' if no_log else '-log10(p)')
if regions:
#"""
# Plot as colored background
if len(new_bounds) < 32:
for s, e in new_bounds:
ax.axvspan(s - 2, e + 2, facecolor='#EA352B',
ec='#EA352B', alpha=0.3, zorder=0)
#"""
# plot as points.
rxs, rys, rcs = zip(*region_xys)
if not no_log: rys = -np.log10(rys)
ax.scatter(rxs, rys,
# s=rys ** 1.3, # size by -log10(p)
s = 6,
c=rcs, edgecolors=rcs,
zorder=2)
if lines:
ax.vlines(xs, 0, ys, colors=cs, alpha=0.5)
else:
alpha = 0.8 if len(xs) < 10000 else 0.6
edgecolors = 'k' if len(xs) < 10000 else 'none'
ax.scatter(xs, ys, s=3.5, c=cs, edgecolors=edgecolors, alpha=alpha, zorder=1)
# plot 0.05 line after multiple testing. always nlog10'ed since
# that's the space we're plotting in.
if bonferonni:
ax.axhline(y=-np.log10(bonferonni_p), color='0.5', linewidth=2)
#plt.axis('tight')
if max(xs) - min(xs) > 10000:
plt.xlim(0, xs[-1])
else:
plt.xlim(xs[0], xs[-1])
plt.ylim(ymin=0)
if ymax is not None: plt.ylim(ymax=ymax)
plt.xticks([c[1] for c in chrom_centers],
[c[0].replace('chr', '') for c in chrom_centers], rotation=-90, size=8.5)
#plt.show()
print >>sys.stderr, "Bonferonni-corrected p-value for %i rows: %.3g" \
% (nrows, 0.05 / nrows)
print >>sys.stderr, "values less than Bonferonni-corrected p-value: %i " \
% (ys > -np.log10(bonferonni_p)).sum()
if subplots:
pys = np.sort(10**-ys) # convert back to actual p-values
gc = genomic_control(pys)
ax_qq = f.add_axes((0.74, 0.12, 0.22, 0.22), alpha=0.2)
ax_qq.text(0.03, 0.88, r'$\lambda : %.3f$' % gc, transform=ax_qq.transAxes)
qqplot(ys, ax_qq)
ax_hist = f.add_axes((0.12, 0.12, 0.22, 0.22), frameon=True, alpha=0.6)
hist(pys, ax_hist)
print >>sys.stderr, "saving to: %s" % image_path
f.tight_layout()
plt.savefig(image_path)
return image_path
def manhattan(fname,
col_num,
image_path,
no_log,
colors,
title,
lines,
ymax,
bonferonni=False,
regions=None,
subplots=False):
"""
regions is keyed by chromosome with [(start, stop), ...] extents of
the regions to highlight
"""
xs, ys, cs = [], [], []
region_xys = [] # highlight certain regions.
colors = cycle(colors)
chrom_centers = []
last_x = 0
nrows = 0
giter = [(seqid, list(rlist)) for seqid, rlist \
in groupby(bediter(fname, col_num), key=itemgetter('chrom'))]
region_xs, region_ys = [], []
new_bounds = []
rcolors = cycle(('#AE2117', '#EA352B'))
for seqid, rlist in sorted(giter, cmp=chr_cmp):
color = colors.next()
nrows += len(rlist)
# since chroms are on the same plot. add this chrom to the end of the
# last chrom
rcolor = rcolors.next()
region_xs = [last_x + r['start'] for r in rlist]
xs.extend(region_xs)
ys.extend([r['p'] for r in rlist])
cs.extend([color] * len(rlist))
if regions and seqid in regions:
regions_bounds = regions[seqid]
if len(regions_bounds) < 500:
region_xys.extend([(last_x + r['start'], r['p'], rcolor) for r in rlist \
if any((s - 1 <= r['start'] <= e + 1) for s, e in regions_bounds)])
else:
sys.stderr.write("regions for %s > 500, not plotting\n" %
seqid)
# adjust the bounds of each region based on chrom.
new_bounds.extend([(last_x + s, last_x + e)
for s, e in regions_bounds])
# save the middle of the region to place the label
chrom_centers.append((seqid, (region_xs[0] + region_xs[-1]) / 2))
# keep track so that chrs don't overlap.
last_x = xs[-1]
xs = np.array(xs)
ys = np.array(ys) if no_log else -np.log10(ys)
plt.close()
f, ax = plt.subplots(1, figsize=(10, 6))
bonferonni_p = 0.05 / nrows
if title is not None:
plt.title(title)
ax.set_ylabel('' if no_log else '-log10(p)')
if regions:
#"""
# Plot as colored background
if len(new_bounds) < 32:
for s, e in new_bounds:
ax.axvspan(s - 2,
e + 2,
facecolor='#EA352B',
ec='#EA352B',
alpha=0.3,
zorder=0)
#"""
# plot as points.
rxs, rys, rcs = zip(*region_xys)
if not no_log: rys = -np.log10(rys)
ax.scatter(
rxs,
rys,
# s=rys ** 1.3, # size by -log10(p)
s=6,
c=rcs,
edgecolors=rcs,
zorder=2)
if lines:
ax.vlines(xs, 0, ys, colors=cs, alpha=0.5)
else:
alpha = 0.8 if len(xs) < 10000 else 0.6
edgecolors = 'k' if len(xs) < 10000 else 'none'
ax.scatter(xs,
ys,
s=3.5,
c=cs,
edgecolors=edgecolors,
alpha=alpha,
zorder=1)
# plot 0.05 line after multiple testing. always nlog10'ed since
# that's the space we're plotting in.
if bonferonni:
ax.axhline(y=-np.log10(bonferonni_p), color='0.5', linewidth=2)
#plt.axis('tight')
if max(xs) - min(xs) > 10000:
plt.xlim(0, xs[-1])
else:
plt.xlim(xs[0], xs[-1])
plt.ylim(ymin=0)
if ymax is not None: plt.ylim(ymax=ymax)
plt.xticks([c[1] for c in chrom_centers],
[c[0].replace('chr', '') for c in chrom_centers],
rotation=-90,
size=8.5)
#plt.show()
print >>sys.stderr, "Bonferonni-corrected p-value for %i rows: %.3g" \
% (nrows, 0.05 / nrows)
print >>sys.stderr, "values less than Bonferonni-corrected p-value: %i " \
% (ys > -np.log10(bonferonni_p)).sum()
if subplots:
pys = np.sort(10**-ys) # convert back to actual p-values
gc = genomic_control(pys)
ax_qq = f.add_axes((0.74, 0.12, 0.22, 0.22), alpha=0.2)
ax_qq.text(0.03,
0.88,
r'$\lambda : %.3f$' % gc,
transform=ax_qq.transAxes)
qqplot(ys, ax_qq)
ax_hist = f.add_axes((0.12, 0.12, 0.22, 0.22), frameon=True, alpha=0.6)
hist(pys, ax_hist)
print >> sys.stderr, "saving to: %s" % image_path
f.tight_layout()
plt.savefig(image_path)
return image_path
def manhattan(fname, col_num, image_path, no_log, colors, title, lines, ymax, bonferonni=False, regions=None):
"""
regions is keyed by chromosome with [(start, stop), ...] extents of
the regions to highlight
"""
xs, ys, cs = [], [], []
region_xys = [] # highlight certain regions.
colors = cycle(colors)
chrom_centers = []
last_x = 0
nrows = 0
giter = [(seqid, list(rlist)) for seqid, rlist in groupby(bediter(fname, col_num), key=itemgetter("chrom"))]
region_xs, region_ys = [], []
new_bounds = []
for seqid, rlist in sorted(giter, cmp=chr_cmp):
color = colors.next()
nrows += len(rlist)
# since chroms are on the same plot. add this chrom to the end of the
# last chrom
region_xs = [last_x + r["start"] for r in rlist]
xs.extend(region_xs)
ys.extend([r["p"] for r in rlist])
cs.extend([color] * len(rlist))
if regions and seqid in regions:
regions_bounds = regions[seqid]
region_xys.extend(
[(last_x + r["start"], r["p"]) for r in rlist if any((s <= r["start"] <= e) for s, e in regions_bounds)]
)
# adjust the bounds of each region based on chrom.
new_bounds.extend([(last_x + s, last_x + e) for s, e in regions_bounds])
# save the middle of the region to place the label
chrom_centers.append((seqid, (region_xs[0] + region_xs[-1]) / 2))
# keep track so that chrs don't overlap.
last_x = xs[-1]
xs = np.array(xs)
ys = np.array(ys) if no_log else -np.log10(ys)
plt.close()
f = plt.figure()
ax = f.add_axes((0.1, 0.09, 0.88, 0.85))
bonferonni_p = 0.05 / nrows
if title is not None:
plt.title(title)
ax.set_ylabel("" if no_log else "-log10(p)")
if regions:
for s, e in new_bounds:
# ax.axvspan(s - 55, e + 10, facecolor='#f30000', ec='#f30000', alpha=0.3,
# zorder=0)
ax.axvspan(s - 55, e + 10, facecolor="#222222", ec="#222222", alpha=0.3, zorder=0)
if lines:
ax.vlines(xs, 0, ys, colors=cs, alpha=0.5)
else:
ax.scatter(xs, ys, s=3.5, c=cs, edgecolors="none", alpha=0.6, zorder=1)
# plot 0.05 line after multiple testing. always nlog10'ed since
# that's the space we're plotting in.
if bonferonni:
ax.axhline(y=-np.log10(bonferonni_p), color="0.5", linewidth=2)
plt.axis("tight")
plt.xlim(0, xs[-1])
plt.ylim(ymin=0)
if ymax is not None:
plt.ylim(ymax=ymax)
plt.xticks([c[1] for c in chrom_centers], [c[0] for c in chrom_centers], rotation=-90, size=8.5)
# plt.show()
print >>sys.stderr, "Bonferonni-corrected p-value for %i rows: %.3g" % (nrows, 0.05 / nrows)
print >>sys.stderr, "values less than Bonferonni-corrected p-value: %i " % (ys > -np.log10(bonferonni_p)).sum()
if False:
ax_qq = f.add_axes((0.74, 0.12, 0.22, 0.22), alpha=0.2)
pys = np.sort(10 ** -ys) # convert back to actual p-values
qqplot(ys, ax_qq)
ax_hist = f.add_axes((0.12, 0.12, 0.22, 0.22), frameon=True, alpha=0.6)
hist(pys, ax_hist)
print >>sys.stderr, "saving to: %s" % image_path
plt.savefig(image_path)
return image_path
def pipeline(col_num,
step,
dist,
acf_dist,
prefix,
threshold,
seed,
bed_files,
mlog=True,
region_filter_p=1,
region_filter_n=None,
genome_control=False,
db=None,
use_fdr=True):
sys.path.insert(0, op.join(op.dirname(__file__), ".."))
from cpv import acf, slk, fdr, peaks, region_p, stepsize, filter
from cpv._common import genome_control_adjust, genomic_control, bediter
import operator
if step is None:
step = min(acf_dist, stepsize.stepsize(bed_files, col_num))
print >> sys.stderr, "calculated stepsize as: %i" % step
lags = range(1, acf_dist, step)
lags.append(lags[-1] + step)
prefix = prefix.rstrip(".")
putative_acf_vals = acf.acf(bed_files,
lags,
col_num,
simple=False,
mlog=mlog)
acf_vals = []
# go out to max requested distance but stop once an autocorrelation
# < 0.05 is added.
for a in putative_acf_vals:
# a is ((lmin, lmax), (corr, N))
# this heuristic seems to work. stop just above the 0.08 correlation
# lag.
if a[1][0] < 0.04 and len(acf_vals) > 2: break
acf_vals.append(a)
if a[1][0] < 0.04 and len(acf_vals): break
# save the arguments that this was called with.
with open(prefix + ".args.txt", "w") as fh:
print >> fh, " ".join(sys.argv[1:]) + "\n"
import datetime
print >> fh, "date: %s" % datetime.datetime.today()
from .__init__ import __version__
print >> fh, "version:", __version__
with open(prefix + ".acf.txt", "w") as fh:
acf_vals = acf.write_acf(acf_vals, fh)
print >> sys.stderr, "wrote: %s" % fh.name
print >> sys.stderr, "ACF:\n", open(prefix + ".acf.txt").read()
spvals, opvals = [], []
with ts.nopen(prefix + ".slk.bed.gz", "w") as fhslk:
fhslk.write('#chrom\tstart\tend\tp\tregion-p\n')
for row in slk.adjust_pvals(bed_files, col_num, acf_vals):
fhslk.write("%s\t%i\t%i\t%.4g\t%.4g\n" % row)
opvals.append(row[-2])
spvals.append(row[-1])
print >> sys.stderr, "# original lambda: %.2f" % genomic_control(opvals)
del opvals
gc_lambda = genomic_control(spvals)
print >> sys.stderr, "wrote: %s with lambda: %.2f" % (fhslk.name,
gc_lambda)
if genome_control:
fhslk = ts.nopen(prefix + ".slk.gc.bed.gz", "w")
adj = genome_control_adjust(
[d['p'] for d in bediter(prefix + ".slk.bed.gz", -1)])
for i, line in enumerate(ts.nopen(prefix + ".slk.bed.gz")):
print >> fhslk, "%s\t%.5g" % (line.rstrip("\r\n"), adj[i])
fhslk.close()
print >> sys.stderr, "wrote: %s" % fhslk.name
with ts.nopen(prefix + ".fdr.bed.gz", "w") as fh:
fh.write('#chrom\tstart\tend\tp\tregion-p\tregion-q\n')
for bh, l in fdr.fdr(fhslk.name, -1):
fh.write("%s\t%.4g\n" % (l.rstrip("\r\n"), bh))
print >> sys.stderr, "wrote: %s" % fh.name
fregions = prefix + ".regions.bed.gz"
with ts.nopen(fregions, "w") as fh:
list(
peaks.peaks(prefix + ".fdr.bed.gz", -1 if use_fdr else -2,
threshold, seed, dist, fh, operator.le))
n_regions = sum(1 for _ in ts.nopen(fregions))
print >> sys.stderr, "wrote: %s (%i regions)" % (fregions, n_regions)
if n_regions == 0:
sys.exit()
with ts.nopen(prefix + ".regions-p.bed.gz", "w") as fh:
N = 0
fh.write("#chrom\tstart\tend\tmin_p\tn_probes\tz_p\tz_sidak_p\n")
# use -2 for original, uncorrected p-values in slk.bed
for region_line, slk_p, slk_sidak_p, sim_p in region_p.region_p(
prefix + ".slk.bed.gz", prefix + ".regions.bed.gz", -2, step):
fh.write("%s\t%.4g\t%.4g\n" % (region_line, slk_p, slk_sidak_p))
fh.flush()
N += int(slk_sidak_p < 0.05)
print >>sys.stderr, "wrote: %s, (regions with corrected-p < 0.05: %i)" \
% (fh.name, N)
regions_bed = fh.name
header = ts.header(bed_files[0])
#if all(h in header for h in ('t', 'start', 'end')):
if region_filter_n is None: region_filter_n = 0
with ts.nopen(prefix + ".regions-t.bed", "w") as fh:
N = 0
for i, toks in enumerate(
filter.filter(bed_files[0], regions_bed, p_col_name=col_num)):
if i == 0: toks[0] = "#" + toks[0]
else:
if float(toks[6]) > region_filter_p: continue
if int(toks[4]) < region_filter_n: continue
#if region_filter_t and "/" in toks[7]:
# # t-pos/t-neg. if the lower one is > region_filter_t?
# vals = map(int, toks[7].split("/"))
# if min(vals) > region_filter_t: continue
N += 1
print >> fh, "\t".join(toks)
print >>sys.stderr, ("wrote: %s, (regions with region-p "
"< %.3f and n-probes >= %i: %i)") \
% (fh.name, region_filter_p, region_filter_n, N)
try:
from cpv import manhattan
regions = manhattan.read_regions(fh.name)
manhattan.manhattan(prefix + ".slk.bed.gz",
3,
prefix.rstrip(".") + ".manhattan.png",
False, ['#959899', '#484B4C'],
"",
False,
None,
regions=regions,
bonferonni=False)
except ImportError:
pass # they dont have matplotlib
if db is not None:
from cruzdb import Genome
g = Genome(db)
lastf = fh.name
with open(prefix + ".anno.%s.bed" % db, "w") as fh:
fh.write('#')
g.annotate(lastf, ("refGene", "cpgIslandExt"),
out=fh,
feature_strand=True,
parallel=len(spvals) > 500)
print >> sys.stderr, "wrote: %s annotated with %s" % (fh.name, db)
def pipeline(col_num, step, dist, prefix, threshold, seed, bed_files, mlog=False,
region_filter_p=1, region_filter_n=1, genome_control=False, db=None):
sys.path.insert(0, op.join(op.dirname(__file__), ".."))
from cpv import acf, slk, fdr, peaks, region_p, stepsize, filter
from cpv._common import genome_control_adjust, genomic_control, bediter
import operator
if step is None:
step = stepsize.stepsize(bed_files, col_num)
print >>sys.stderr, "calculated stepsize as: %i" % step
lags = range(1, dist, step)
lags.append(lags[-1] + step)
prefix = prefix.rstrip(".")
#if genome_control:
# with open(prefix + ".adj.bed", "w") as fh:
# genome_control_adjust_bed(bed_files, col_num, fh)
# bed_files = [fh.name]
putative_acf_vals = acf.acf(bed_files, lags, col_num, simple=False,
mlog=mlog)
acf_vals = []
# go out to max requested distance but stop once an autocorrelation
# < 0.05 is added.
for a in putative_acf_vals:
# a is ((lmin, lmax), (corr, N))
# this heuristic seems to work. stop just above the 0.08 correlation
# lag.
if a[1][0] < 0.04 and len(acf_vals) > 2: break
acf_vals.append(a)
if a[1][0] < 0.04 and len(acf_vals): break
# save the arguments that this was called with.
with open(prefix + ".args.txt", "w") as fh:
print >>fh, " ".join(sys.argv[1:]) + "\n"
import datetime
print >>fh, "date: %s" % datetime.datetime.today()
with open(prefix + ".acf.txt", "w") as fh:
acf_vals = acf.write_acf(acf_vals, fh)
print >>sys.stderr, "wrote: %s" % fh.name
print >>sys.stderr, "ACF:\n", open(prefix + ".acf.txt").read()
spvals, opvals = [], []
with open(prefix + ".slk.bed", "w") as fhslk:
for row in slk.adjust_pvals(bed_files, col_num, acf_vals):
fhslk.write("%s\t%i\t%i\t%.4g\t%.4g\n" % row)
opvals.append(row[-2])
spvals.append(row[-1])
print >>sys.stderr, "# original lambda: %.2f" % genomic_control(opvals)
del opvals
gc_lambda = genomic_control(spvals)
print >>sys.stderr, "wrote: %s with lambda: %.2f" % (fhslk.name, gc_lambda)
if genome_control:
fhslk = open(prefix + ".slk.gc.bed", "w")
adj = genome_control_adjust([d['p'] for d in bediter(prefix + ".slk.bed", -1)])
for i, line in enumerate(open(prefix + ".slk.bed")):
print >>fhslk, "%s\t%.5g" % (line.rstrip("\r\n"), adj[i])
fhslk.close()
print >>sys.stderr, "wrote: %s" % fhslk.name
with open(prefix + ".fdr.bed", "w") as fh:
for bh, l in fdr.fdr(fhslk.name, -1):
fh.write("%s\t%.4g\n" % (l.rstrip("\r\n"), bh))
print >>sys.stderr, "wrote: %s" % fh.name
fregions = prefix + ".regions.bed"
with open(fregions, "w") as fh:
list(peaks.peaks(prefix + ".fdr.bed", -1, threshold, seed,
step, fh, operator.le))
n_regions = sum(1 for _ in open(fregions))
print >>sys.stderr, "wrote: %s (%i regions)" % (fregions, n_regions)
with open(prefix + ".regions-p.bed", "w") as fh:
N = 0
fh.write("#chrom\tstart\tend\tmin_p\tn_probes\tslk_p\tslk_sidak_p\n")
# use -2 for original, uncorrected p-values in slk.bed
for region_line, slk_p, slk_sidak_p, sim_p in region_p.region_p(
prefix + ".slk.bed",
prefix + ".regions.bed", -2,
0, step, mlog=mlog):
fh.write("%s\t%.4g\t%.4g\n" % (region_line, slk_p, slk_sidak_p))
fh.flush()
N += int(slk_sidak_p < 0.05)
print >>sys.stderr, "wrote: %s, (regions with corrected-p < 0.05: %i)" \
% (fh.name, N)
regions_bed = fh.name
header = (gzip.open(bed_files[0]) if bed_files[0].endswith(".gz")
else open(bed_files[0])).next().split("\t")
if all(h in header for h in ('t', 'start', 'end')):
with open(prefix + ".regions-t.bed", "w") as fh:
N = 0
for i, toks in enumerate(filter.filter(bed_files[0], regions_bed,
p_col_name=col_num)):
if i == 0: toks[0] = "#" + toks[0]
else:
if float(toks[6]) > region_filter_p: continue
if int(toks[4]) < region_filter_n: continue
N += 1
print >>fh, "\t".join(toks)
print >>sys.stderr, ("wrote: %s, (regions with region-p"
"< %.3f and n-probes >= %i: %i)") \
% (fh.name, region_filter_p, region_filter_n, N)
try:
from cpv import manhattan
regions = manhattan.read_regions(fh.name)
manhattan.manhattan(prefix + ".slk.bed", 3, prefix.rstrip(".") + ".manhattan.png",
False, ['#959899', '#484B4C'], "", False, None,
regions=regions, bonferonni=True)
except ImportError:
pass # they dont have matplotlib
if db is not None:
from cruzdb import Genome
g = Genome(db)
lastf = fh.name
with open(prefix + ".anno.%s.bed" % db, "w") as fh:
g.annotate(lastf, ("refGene", "cpgIslandExt", "cytoBand"), out=fh,
feature_strand=True, parallel=len(spvals) > 500)
print >>sys.stderr, "wrote: %s annotated with %s" % (fh.name, db)