def align2local(self, i, clamp=False):
if clamp:
return self.align2localLookup[int(
util.clamp(i, 0,
len(self.align2localLookup) - 1))]
else:
return self.align2localLookup[i]
def local2align(self, i, clamp=False):
if clamp:
return self.local2alignLookup[int(
util.clamp(i, 0,
len(self.local2alignLookup) - 1))]
else:
return self.local2alignLookup[i]
def percentile(vals, perc, rounding=-1, sort=True):
"""Give the value at a percentile
rounding -- round down if -1 or round up for 1
"""
if sort:
vals2 = sorted(vals)
else:
vals2 = vals
n = len(vals2)
if rounding == -1:
return vals2[util.clamp(int(perc * n), 0, n - 1)]
elif rounding == 1:
return vals2[util.clamp(int(ceil(perc * n)), 0, n - 1)]
else:
raise Exception("rounding must be 1 or -1")
def percentile(vals, perc, rounding=-1, sort=True):
"""Give the value at a percentile
rounding -- round down if -1 or round up for 1
"""
if sort:
vals2 = sorted(vals)
else:
vals2 = vals
n = len(vals2)
if rounding == -1:
return vals2[util.clamp(int(perc * n), 0, n-1)]
elif rounding == 1:
return vals2[util.clamp(int(ceil(perc * n)), 0, n-1)]
else:
raise Exception("rounding must be 1 or -1")
def getseq(self, key, start=1, end=None, strand=1):
"""Get a sequence (or subsequence) by key"""
val = SeqDict.__getitem__(self, key)
if val is None:
# if val == None, then we are using fasta indexing
return self.index.get(key, start, end, strand)
else:
start = util.clamp(start, 1, None)
end = util.clamp(end, 1, None)
val = val[start - 1:end]
# reverse complement if needed
if strand == -1:
val = _revcomp(val)
return val
def getseq(self, key, start=1, end=None, strand=1):
"""Get a sequence (or subsequence) by key"""
val = SeqDict.__getitem__(self, key)
if val is None:
# if val == None, then we are using fasta indexing
return self.index.get(key, start, end, strand)
else:
start = util.clamp(start, 1, None)
end = util.clamp(end, 1, None)
val = val[start-1:end]
# reverse complement if needed
if strand == -1:
val = _revcomp(val)
return val
def update(self):
assert self.view != None, "Track view not initialized"
win = self.get_window()
if not self.shown or not self.multiscale.same_view():
self.shown = True
x, y = self.pos
start2 = self.view.start
start = int(
max(0, start2 - 1, self.multiscale.worldx1 - x + start2))
end = int(
min(len(self.xdata), self.view.end,
self.multiscale.worldx2 - x + start2))
step = max(1, (end - start) // 400)
vis = []
vis2 = []
for i in xrange(start, end, step):
dat = self.ydata[i:i + step]
assert len(dat) > 0, (start, end, step)
y1 = min(dat)
y2 = max(dat)
#y = self.ydata[i]
y1 = (util.clamp(y1, .33, .66) - .33) / .33
y2 = (util.clamp(y2, .33, .66) - .33) / .33
vis.extend([self.xdata[i], y2 * self.size[1]])
vis2.extend([self.xdata[i], y1 * self.size[1]])
# draw curve on middle of base (.5)
self.gid = win.replace_group(
self.gid,
group(
translate(
x - self.view.start + .5, y, color(0, 1, 0),
line_strip(*vis), line_strip(*vis2), color(0, 0, 0),
lines(self.view.start - 0.5, 0, self.view.end + 0.5, 0,
self.view.start - 0.5, self.size[1],
self.view.end + 0.5, self.size[1]))))
def update(self):
assert self.view != None, "Track view not initialized"
win = self.get_window()
if not self.shown or not self.multiscale.same_view():
self.shown = True
x, y = self.pos
start2 = self.view.start
start = int(max(0, start2-1, self.multiscale.worldx1-x+start2))
end = int(min(len(self.xdata), self.view.end, self.multiscale.worldx2-x+start2))
step = max(1, (end - start) // 400)
vis = []
vis2 = []
for i in xrange(start, end, step):
dat = self.ydata[i:i+step]
assert len(dat) > 0, (start, end, step)
y1 = min(dat)
y2 = max(dat)
#y = self.ydata[i]
y1 = (util.clamp(y1, .33, .66) - .33) / .33
y2 = (util.clamp(y2, .33, .66) - .33) / .33
vis.extend([self.xdata[i], y2 * self.size[1]])
vis2.extend([self.xdata[i], y1 * self.size[1]])
# draw curve on middle of base (.5)
self.gid = win.replace_group(self.gid,
group(translate(x - self.view.start + .5, y,
color(0,1,0),
line_strip(* vis),
line_strip(* vis2),
color(0,0,0),
lines(self.view.start - 0.5, 0, self.view.end + 0.5, 0,
self.view.start - 0.5, self.size[1],
self.view.end + 0.5, self.size[1]))))
def midroot_recon(tree, stree, recon, events, params, generate):
node1, node2 = tree.root.children
specs1 = []
specs2 = []
# find nearest specs/genes
def walk(node, specs):
if events[node] == "dup":
for child in node.children:
walk(child, specs)
else:
specs.append(node)
#walk(node1, specs1)
#walk(node2, specs2)
specs1 = node1.leaves()
specs2 = node2.leaves()
def getDists(start, end):
exp_dist = 0
obs_dist = 0
sstart = recon[start]
send = recon[end]
while sstart != send:
exp_dist += params[sstart.name][0]
sstart = sstart.parent
while start != end:
obs_dist += start.dist
start = start.parent
return exp_dist, obs_dist / generate
diffs1 = []
for spec in specs1:
if events[tree.root] == "spec":
exp_dist1, obs_dist1 = getDists(spec, tree.root)
else:
exp_dist1, obs_dist1 = getDists(spec, node1)
diffs1.append(obs_dist1 - exp_dist1)
diffs2 = []
for spec in specs2:
if events[tree.root] == "spec":
exp_dist2, obs_dist2 = getDists(spec, tree.root)
else:
exp_dist2, obs_dist2 = getDists(spec, node2)
diffs2.append(obs_dist2 - exp_dist2)
totdist = (node1.dist + node2.dist) / generate
left = node1.dist - stats.mean(diffs1)
right = totdist - node2.dist + stats.mean(diffs2)
#print diffs1, diffs2
#print stats.mean(diffs1), stats.mean(diffs2)
mid = util.clamp((left + right) / 2.0, 0, totdist)
node1.dist = mid * generate
node2.dist = (totdist - mid) * generate
def align2local(self, i, clamp=False):
if clamp:
return self.align2localLookup[
int(util.clamp(i, 0, len(self.align2localLookup)-1))]
else:
return self.align2localLookup[i]
def local2align(self, i, clamp=False):
if clamp:
return self.local2alignLookup[
int(util.clamp(i, 0, len(self.local2alignLookup)-1))]
else:
return self.local2alignLookup[i]
