def iter_chroms(hits):
"""
Returns an iterator of iterators it, such that each it iterates over
hits from the same species and chromosome.
"""
hits = util.PushIter(hits)
try:
hit = hits.next()
except StopIteration:
# no hits to iterate
return
# initiate which species and chrom we are going to start with
last_sp = [hit[0].species]
last_chrom = [hit[0].seqname]
hits.push(hit)
def inner_iter(hits):
"""An iterator of hits from only one species, chromome"""
for hit in hits:
if hit[0].species != last_sp[0] or hit[0].seqname != last_chrom[0]:
# if species,chrom changes, push hit back and return
last_sp[0] = hit[0].species
last_chrom[0] = hit[0].seqname
hits.push(hit)
return
yield hit
while hits.peek(None) != None:
yield inner_iter(hits)
def __init__(self, filename, parse_trees=False, apply_spr=False):
if isinstance(filename, basestring):
# read SMC from file
self._filename = filename
self._infile = iter_smc_file(filename,
parse_trees=parse_trees,
apply_spr=apply_spr)
self._stream = util.PushIter(self._infile)
else:
# read SMC from list of items
self._filename = None
self._infile = None
self._stream = util.PushIter(filename)
# read header
header_tags = ("NAMES", "REGION")
self.header = {}
while self._stream.peek({"tag": ""})["tag"] in header_tags:
self.header.update(self._stream.next())
del self.header["tag"]
def iter_windows(hits, radius):
"""Iterate through blast hits using a window with a radius in the
query genome"""
hits = util.PushIter(hits)
cache = LinkedList()
upstream = set()
downstream = set()
try:
center = hits.next()
except StopIteration:
return
while True:
# discard anyone in the upstream that is not within radius distance
for hit in list(upstream):
if hit[0].end + radius < center[0].start:
upstream.remove(hit)
# populate downstream with all regions within in radius
for hit in hits:
if hit[0].start - radius > center[0].end:
hits.push(hit)
break
downstream.add(hit)
cache.append(hit)
yield (center, upstream, downstream)
# populate upstream
upstream.add(center)
# move center to next hit
try:
center = cache.pop_front()
except IndexError:
break
# remove new center from downstream
downstream.remove(center)
def show_tree_track(tree_track,
mut=None,
show_labels=False,
use_blocks=False,
branch_click=None):
"""
tree_track = [((start, end), tree), ...]
"""
def draw_labels(tree, layout):
return group(*[
text_clip(leaf.name, layout[leaf][0], layout[leaf][1], 1,
layout[leaf][1] + 1e4, 4, 20, "middle", "left")
for leaf in tree.leaves()
])
def branch_hotspot(node, parent, x, y, y2):
def func():
branch_click(node, parent)
return hotspot("click", x - .5, y, x + .5, y2, func)
def print_branch(node, parent):
print "node", node.name
tree_track = iter(tree_track)
if mut:
mut = util.PushIter(mut)
block, tree = tree_track.next()
if branch_click is True:
branch_click = print_branch
win = summon.Window()
treex = 0
step = 2
treewidth = len(list(tree.leaves())) + step
def trans_camera(win, x, y):
v = win.get_visible()
win.set_visible(v[0] + x, v[1] + y, v[2] + x, v[3] + y, "exact")
win.set_binding(input_key("]"), lambda: trans_camera(win, treewidth, 0))
win.set_binding(input_key("["), lambda: trans_camera(win, -treewidth, 0))
for block, tree in chain([(block, tree)], tree_track):
pos = block[0]
print pos
layout = treelib.layout_tree(tree, xscale=1, yscale=1)
treelib.layout_tree_vertical(layout, leaves=0)
g = win.add_group(
translate(
treex, 0, color(1, 1, 1),
sumtree.draw_tree(tree, layout, vertical=True),
(draw_labels(tree, layout) if show_labels else group()),
text_clip("%d-%d" % (block[0], block[1]), treewidth * .05, 0,
treewidth * .95, -max(l[1] for l in layout.values()),
4, 20, "center", "top")))
clicking = group()
g.append(clicking)
# hotspots
if branch_click:
for node in tree:
if node.parent:
x, y = layout[node]
x2, y2 = layout[node.parent]
clicking.append(branch_hotspot(node, node.parent, x, y,
y2))
#win.add_group(clicking)
# draw mut
if mut:
for mpos, age, chroms in mut:
if block[0] < mpos < block[1]:
node = arglib.split_to_tree_branch(tree, chroms)
parent = node.parent
if node and parent:
t = random.uniform(layout[node][1], layout[parent][1])
nx, ny = layout[node]
win.add_group(draw_mark(treex + nx, t, col=(0, 0, 1)))
elif mpos > block[1]:
mut.push((mpos, age, chroms))
break
treex += treewidth
#win.set_visible(* win.get_root().get_bounding() + ("exact",))
win.home("exact")
return win