def draw_trace(self, dotplot):
vis = []
# get current view
view = dotplot.win.get_visible()
for region in self.regions1:
if region in dotplot.layout1:
start = dotplot.layout1[region]
else:
continue
# only draw regions in view
end = start + region.length()
if util.overlap(view[0], view[2], start, end):
vis.extend([color(* self.trace_color),
lines(start, 0, start, dotplot.plot_size[1]),
shapes.box(start, 0, end, dotplot.plot_size[1])])
for region in self.regions2:
if region in dotplot.layout2:
start = dotplot.layout2[region]
else:
continue
# only draw regions in view
end = start + region.length()
if util.overlap(view[1], view[3], start, end):
vis.extend([color(* self.trace_color),
lines(0, start, dotplot.plot_size[0], start),
shapes.box(0, start, dotplot.plot_size[0], end)])
return group(*vis)
def overlap(region1, region2):
"""Tests whether two regions overlap"""
return region1.seqname == region2.seqname and \
region1.species == region2.species and \
util.overlap(region1.start, region1.end,
region2.start, region2.end)
def overlap(region1, region2):
"""Tests whether two regions overlap"""
return region1.seqname == region2.seqname and \
region1.species == region2.species and \
util.overlap(region1.start, region1.end,
region2.start, region2.end)
def find_syntenic_neighbors(hits, radius, radius2=None):
"""
For each hit find the neighboring hits that are syntenic.
hits -- iterable of tuples (region1, region2, extra)
radius -- radius of window in query genome
radius2 -- radius of window in subject genome (default=radius)
hits must be sorted by query region species, chrom, and start
"""
if radius2 is None:
radius2 = radius
for hits2 in iter_chroms(hits):
for center, upstream, downstream in iter_windows(hits2, radius):
start = center[1].start - radius2
end = center[1].end + radius2
syntenic = []
for hit in chain(upstream, downstream):
# determine which subjects are wihtin the window of
if (hit[1].species == center[1].species
and hit[1].seqname == center[1].seqname and
util.overlap(start, end, hit[1].start, hit[1].end)):
syntenic.append(hit)
yield (center, syntenic)
def get(self, species, chrom, start, end):
records = []
for record in self.lookup[(species, chrom)]:
if util.overlap(start, end, record["start"], record["end"]):
records.append(record)
return records
def get(self, species, chrom, start, end):
records = []
for record in self.lookup[(species, chrom)]:
if util.overlap(start, end, record["start"], record["end"]):
records.append(record)
return records
def layout_regions(self, layout, chromLookup, regions, chromLayout):
for region in regions:
chrom = chromLookup.get((region.species, region.seqname), None)
if chrom in chromLayout and \
util.overlap(chrom.start, chrom.end, region.start, region.end):
chrompos = chromLayout[chrom]
layout[region] = chrompos + region.start - chrom.start
def layout_regions(self, layout, chromLookup, regions, chromLayout):
for region in regions:
chrom = chromLookup.get((region.species, region.seqname), None)
if chrom in chromLayout and \
util.overlap(chrom.start, chrom.end, region.start, region.end):
chrompos = chromLayout[chrom]
layout[region] = chrompos + region.start - chrom.start
def filter_blocks(self, blocks, ref_chrom, start, end):
"""Filter blocks for those that contain the chromosome.
Also the matching side of the block is returned
"""
for block in blocks:
if ((block.region1.species, block.region1.seqname)
not in self.chroms_lookup
or (block.region2.species, block.region2.seqname)
not in self.chroms_lookup):
continue
if (block.region1.seqname == ref_chrom.seqname and util.overlap(
block.region1.start, block.region1.end, start, end)):
yield (block, 0)
elif (block.region2.seqname == ref_chrom.seqname and util.overlap(
block.region2.start, block.region2.end, start, end)):
yield (block, 1)
def filter_blocks(self, blocks, ref_chrom, start, end):
"""Filter blocks for those that contain the chromosome.
Also the matching side of the block is returned
"""
for block in blocks:
if ((block.region1.species,
block.region1.seqname) not in self.chroms_lookup or
(block.region2.species,
block.region2.seqname) not in self.chroms_lookup):
continue
if (block.region1.seqname == ref_chrom.seqname and
util.overlap(block.region1.start,
block.region1.end,
start, end)):
yield (block, 0)
elif (block.region2.seqname == ref_chrom.seqname and
util.overlap(block.region2.start,
block.region2.end,
start, end)):
yield (block, 1)
def draw_trace(self, dotplot):
vis = []
# get current view
view = dotplot.win.get_visible()
for region in self.regions1:
if region in dotplot.layout1:
start = dotplot.layout1[region]
else:
continue
# only draw regions in view
end = start + region.length()
if util.overlap(view[0], view[2], start, end):
vis.extend([
color(*self.trace_color),
lines(start, 0, start, dotplot.plot_size[1]),
shapes.box(start, 0, end, dotplot.plot_size[1])
])
for region in self.regions2:
if region in dotplot.layout2:
start = dotplot.layout2[region]
else:
continue
# only draw regions in view
end = start + region.length()
if util.overlap(view[1], view[3], start, end):
vis.extend([
color(*self.trace_color),
lines(0, start, dotplot.plot_size[0], start),
shapes.box(0, start, dotplot.plot_size[0], end)
])
return group(*vis)
def draw(self):
assert self.view != None, "Track view not initialized"
species = self.view.species
chrom = self.view.seqname
start = self.view.start
end = self.view.end
height = self.height
regions = filter(lambda x: x.seqname == chrom and
x.species == species, self.regions)
def click_region(region):
return lambda: self.on_click(region)
if self.style == 'box':
# box style
vis = []
vis2 = []
hotspots = []
names = []
for reg in regions:
if util.overlap(start, end, reg.start, reg.end):
if reg.strand == 1:
# positive strand
bot = 0
top = height
elif reg.strand == -1:
# negative strand
bot = -height
top = 0
else:
bot = -height
top = height
vis.extend([reg.start-start, bot,
reg.end-start+1, bot,
reg.end-start+1, top,
reg.start-start, top])
vis2.extend([reg.start-start, bot,
reg.start-start, top])
if 'ID' in reg.data:
names.append(text_clip(reg.data['ID'],
reg.start-start, bot,
reg.end-start+1, top,
4,
self.textSize))
if self.on_click:
hotspots.append(hotspot("click",
reg.start-start, top,
reg.end-start+1, bot,
click_region(reg)))
return group(translate(
self.pos[0], self.pos[1] + self.size[1] / 2.0,
color(0,0,0), lines(0, 0, end-start+1, 0),
self.color, quads(*vis), lines(*vis2),
group(*hotspots),
self.text_color, *names))
elif self.style == 'line':
# line style
vis = []
for reg in regions:
if util.overlap(start, end, reg.start, reg.end):
if reg.strand != 0:
vis.extend([reg.start-start, 0,
reg.start-start, reg.strand*height])
else:
vis.extent([reg.start-start, -.5 * height,
reg.start-start, .5 * height])
return group(translate(self.pos[0], self.pos[1] + self.size[1] / 2.0,
color(0,0,0), lines(0, 0, end-start+1, 0),
self.color, lines(* vis)))
else:
# custom style
regions2 = (reg for reg in regions
if util.overlap(start, end, reg.start, reg.end))
return group(translate(self.pos[0], self.pos[1] + self.size[1] / 2.0,
self.style(regions2, start)))
def get_region_pos(self, reg):
if reg.seqname == self.view.seqname and \
util.overlap(self.view.start, self.view.end, reg.start, reg.end):
return (self.pos[0] + reg.start - self.view.start, self.pos[1])
else:
return None
def draw(self):
assert self.view != None, "Track view not initialized"
species = self.view.species
chrom = self.view.seqname
start = self.view.start
end = self.view.end
height = self.height
regions = filter(lambda x: x.seqname == chrom and x.species == species,
self.regions)
def click_region(region):
return lambda: self.on_click(region)
if self.style == 'box':
# box style
vis = []
vis2 = []
hotspots = []
names = []
for reg in regions:
if util.overlap(start, end, reg.start, reg.end):
if reg.strand == 1:
# positive strand
bot = 0
top = height
elif reg.strand == -1:
# negative strand
bot = -height
top = 0
else:
bot = -height
top = height
vis.extend([
reg.start - start, bot, reg.end - start + 1, bot,
reg.end - start + 1, top, reg.start - start, top
])
vis2.extend(
[reg.start - start, bot, reg.start - start, top])
if 'ID' in reg.data:
names.append(
text_clip(reg.data['ID'], reg.start - start, bot,
reg.end - start + 1, top, 4,
self.textSize))
if self.on_click:
hotspots.append(
hotspot("click", reg.start - start,
top, reg.end - start + 1, bot,
click_region(reg)))
return group(
translate(self.pos[0], self.pos[1] + self.size[1] / 2.0,
color(0, 0, 0), lines(0, 0, end - start + 1, 0),
self.color, quads(*vis), lines(*vis2),
group(*hotspots), self.text_color, *names))
elif self.style == 'line':
# line style
vis = []
for reg in regions:
if util.overlap(start, end, reg.start, reg.end):
if reg.strand != 0:
vis.extend([
reg.start - start, 0, reg.start - start,
reg.strand * height
])
else:
vis.extent([
reg.start - start, -.5 * height, reg.start - start,
.5 * height
])
return group(
translate(self.pos[0], self.pos[1] + self.size[1] / 2.0,
color(0, 0, 0), lines(0, 0, end - start + 1, 0),
self.color, lines(*vis)))
else:
# custom style
regions2 = (reg for reg in regions
if util.overlap(start, end, reg.start, reg.end))
return group(
translate(self.pos[0], self.pos[1] + self.size[1] / 2.0,
self.style(regions2, start)))
def get_region_pos(self, reg):
if reg.seqname == self.view.seqname and \
util.overlap(self.view.start, self.view.end, reg.start, reg.end):
return (self.pos[0] + reg.start - self.view.start, self.pos[1])
else:
return None