class SeqTrack (Track):
"""Track for displaying a single sequence along the genome"""
def __init__(self, seqs, **options):
options.setdefault("size", [0.0, 0.5])
Track.__init__(self, **options)
self.seqs = seqs
self.shown = False
self.multiscale = Multiscale(marginx=.5, marginy=.5)
def draw(self):
self.shown = False
self.multiscale.init(self.get_window())
# return placeholder group
self.gid = group()
return self.gid
def update(self):
if self.view == None:
raise Exception("Track view not initialized")
win = self.get_window()
view = win.get_visible()
x, y = self.pos
if self.multiscale.atleast(4, .1, view=view):
if not self.shown or \
not self.multiscale.same_view(view):
self.shown = True
start = max(int(self.multiscale.worldx1 - x + self.view.start),
int(self.view.start))
end = min(int(self.multiscale.worldx2 - x + self.view.start),
int(self.view.end))
seq = self.seqs.getseq(self.view.seqname, start, end)
# convert from inclusive to exclusive
end = len(seq) + start - 1
self.gid = win.replace_group(self.gid,
group(translate(x, y,
color(0,0,0),
scale(1, self.size[1],
text_scale(seq, start-self.view.start,
0, end-self.view.start+1, 2,
"left", "bottom")))))
elif self.shown:
self.shown = False
self.gid = win.replace_group(self.gid, group())
class SeqTrack(Track):
"""Track for displaying a single sequence along the genome"""
def __init__(self, seqs, **options):
options.setdefault("size", [0.0, 0.5])
Track.__init__(self, **options)
self.seqs = seqs
self.shown = False
self.multiscale = Multiscale(marginx=.5, marginy=.5)
def draw(self):
self.shown = False
self.multiscale.init(self.get_window())
# return placeholder group
self.gid = group()
return self.gid
def update(self):
if self.view == None:
raise Exception("Track view not initialized")
win = self.get_window()
view = win.get_visible()
x, y = self.pos
if self.multiscale.atleast(4, .1, view=view):
if not self.shown or \
not self.multiscale.same_view(view):
self.shown = True
start = max(int(self.multiscale.worldx1 - x + self.view.start),
int(self.view.start))
end = min(int(self.multiscale.worldx2 - x + self.view.start),
int(self.view.end))
seq = self.seqs.getseq(self.view.seqname, start, end)
# convert from inclusive to exclusive
end = len(seq) + start - 1
self.gid = win.replace_group(
self.gid,
group(
translate(
x, y, color(0, 0, 0),
scale(
1, self.size[1],
text_scale(seq, start - self.view.start, 0,
end - self.view.start + 1, 2,
"left", "bottom")))))
elif self.shown:
self.shown = False
self.gid = win.replace_group(self.gid, group())
class AlignTrack (Track):
def __init__(self, aln, collapse=None, cols=None, color_bases=False,
seqtype=None, show_color_bases=True, show_bases=True,
show_labels=True,
rowspacing=None,
**options):
Track.__init__(self, **options)
self.size = [aln.alignlen(), len(aln)]
self.multiscale = Multiscale(marginx=.5, marginy=.5)
self.collapse = collapse
self.show_color_bases = show_color_bases
self.show_bases = show_bases
self.show_labels = show_labels
self.rowspacing = rowspacing
self.always_color = False
self.color_bases_vis = None
if seqtype == None:
self.seqtype = guessAlign(aln)
else:
self.seqtype = seqtype
if color_bases == True:
if self.seqtype == "dna":
self.color_bases = dna_colors
elif self.seqtype == "pep":
self.color_bases = pep_colors
else:
self.color_bases = color_bases
if collapse != None:
assert collapse in aln.keys()
cols = util.findneq('-', aln[collapse])
if cols != None:
self.aln = alignlib.subalign(aln, cols)
else:
self.aln = aln
def draw(self):
self.text_shown = False
self.multiscale.init(self.get_window())
BASE = 0
GAP = 1
NOBASE = 2
if self.seqtype == "dna":
baseclasses = {'A': BASE, 'C': BASE, 'T': BASE, 'G': BASE,
'-': GAP, 'N': NOBASE, '*': NOBASE, 'X': NOBASE}
elif self.seqtype == "pep":
baseclasses = {'-': GAP, 'N': NOBASE, '*': NOBASE, 'X': NOBASE}
for aa in 'ARNDCEQGHILKMFPSTWYVU':
baseclasses[aa] = BASE
else:
raise Exception("unknown seqtype '%s'" % self.seqtype)
# init row spacing
if self.rowspacing == None:
self.rowspacing = range(len(self.aln))
def getRegions(selectedClass):
boxpts = []
diagpts = []
diagpts2 = []
for row, (key, val) in zip(self.rowspacing, self.aln.iteritems()):
lastbase = None
lastclass = None
lasti = 0
for i in xrange(len(val)+1):
# this extra is being used to handle the case when
# a sequence is all bases
if i < len(val):
base = val[i]
else:
base = '-'
if base not in baseclasses:
baseclass = NOBASE
else:
baseclass = baseclasses[base]
if baseclass == lastclass:
continue
if lastbase != None and lastclass == selectedClass:
boxpts.extend([lasti, -row, lasti, -row-1, i, -row-1, i, -row])
diagpts.extend([i, -row, i, -row-1])
#diagpts.extend([lasti, -row, i, -row-1])
#diagpts2.extend([lasti, -row, lasti, -row-1])
lasti = i
lastbase = base
lastclass = baseclass
return boxpts, diagpts, diagpts2
base_boxpts, base_diagpts, base_diagpts2 = getRegions(BASE)
nobase_boxpts, nobase_diagpts, nobase_diagpts2 = getRegions(NOBASE)
# build labels
if self.show_labels:
labels = []
for i, key in zip(self.rowspacing, self.aln):
labels.append(text_clip(key, -util.INF, -i, 0, -i-1,
4, 12, "middle", "right"))
labelsgroup = group(*labels)
else:
labelsgroup = group()
# build hotspot
click = hotspot("click", 0, 0, self.aln.alignlen(), -self.size[1],
self.on_click_callback)
self.text_group = group()
return group(translate(self.pos[0], self.pos[1] + self.size[1],
color(0, 0, 0),
labelsgroup,
click,
color(.5, .5, .5),
quads(* base_boxpts),
lines(* base_diagpts),
#lines(* base_diagpts2),
color(.7, .2, .2),
quads(* nobase_boxpts),
lines(* nobase_diagpts),
#lines(* nobase_diagpts2),
group(self.text_group)))
def draw_left(self):
labels = []
maxsize = max(map(len, self.aln.keys()))
for i, key in enumerate(self.aln):
labels.append(text_clip(key, -util.INF, -i, 0, -i-1,
4, 12, "middle", "right"))
return group(translate(self.pos[0], self.pos[1] + self.size[1],
color(0,0,0),
#lines(0, 0, 0, -len(self.aln),
# -maxsize, 0, 0, 0,
# -maxsize, -len(self.aln), 0, -len(self.aln)),
*labels))
def update(self):
win = self.get_window()
view = win.get_visible()
size = win.get_size()
x, y = self.pos
mintextSize = 4
minblockSize = 1
color_bases = self.color_bases
if self.multiscale.atleast(minblockSize, .1,
view=view, size=size):
if not self.text_shown or \
not self.multiscale.same_view(view):
self.text_shown = True
start = max(int(self.multiscale.worldx1 - x - 1),
0)
end = max(int(self.multiscale.worldx2 - x), start)
vis = []
vis2 = []
for i, row in enumerate(self.aln.itervalues()):
seq = row[start:end]
seq = seq.replace("-", " ")
# color bases
if self.show_color_bases and color_bases != False:
for j in xrange(len(seq)):
base = seq[j].upper()
if base in color_bases:
vis2.extend([color_bases[base],
quads(start + j, -i,
start + j, -i-1,
start + j+1, -i-1,
start + j+1, -i)])
end2 = start + len(seq)
# draw text
if self.show_bases and \
self.multiscale.atleast(mintextSize, 2,
view=view, size=size):
vis.append(text_scale(seq,
start, -i+1,
end2, -i-1,
"left", "bottom"))
self.text_group = win.replace_group(self.text_group,
group(group(*vis2), color(0,0,0), * vis))
elif self.text_shown:
self.text_shown = False
self.text_group = win.replace_group(self.text_group, group())
def on_click_callback(self):
# TODO: should not rely on get_mouse_pos("world")
win = self.get_window()
x, y = win.get_mouse_pos('world')
x -= self.pos[0]
y = self.size[1] - (y - self.pos[1])
self.on_click(x, y)
def on_click(self, x, y):
y = int(y)
if 0 <= y < len(self.aln):
print self.aln.keys()[y]
class AlignTrack(Track):
def __init__(self,
aln,
collapse=None,
cols=None,
color_bases=False,
seqtype=None,
show_color_bases=True,
show_bases=True,
show_labels=True,
rowspacing=None,
**options):
Track.__init__(self, **options)
self.size = [aln.alignlen(), len(aln)]
self.multiscale = Multiscale(marginx=.5, marginy=.5)
self.collapse = collapse
self.show_color_bases = show_color_bases
self.show_bases = show_bases
self.show_labels = show_labels
self.rowspacing = rowspacing
self.always_color = False
self.color_bases_vis = None
if seqtype == None:
self.seqtype = guessAlign(aln)
else:
self.seqtype = seqtype
if color_bases == True:
if self.seqtype == "dna":
self.color_bases = dna_colors
elif self.seqtype == "pep":
self.color_bases = pep_colors
else:
self.color_bases = color_bases
if collapse != None:
assert collapse in aln.keys()
cols = util.findneq('-', aln[collapse])
if cols != None:
self.aln = alignlib.subalign(aln, cols)
else:
self.aln = aln
def draw(self):
self.text_shown = False
self.multiscale.init(self.get_window())
BASE = 0
GAP = 1
NOBASE = 2
if self.seqtype == "dna":
baseclasses = {
'A': BASE,
'C': BASE,
'T': BASE,
'G': BASE,
'-': GAP,
'N': NOBASE,
'*': NOBASE,
'X': NOBASE
}
elif self.seqtype == "pep":
baseclasses = {'-': GAP, 'N': NOBASE, '*': NOBASE, 'X': NOBASE}
for aa in 'ARNDCEQGHILKMFPSTWYVU':
baseclasses[aa] = BASE
else:
raise Exception("unknown seqtype '%s'" % self.seqtype)
# init row spacing
if self.rowspacing == None:
self.rowspacing = range(len(self.aln))
def getRegions(selectedClass):
boxpts = []
diagpts = []
diagpts2 = []
for row, (key, val) in zip(self.rowspacing, self.aln.iteritems()):
lastbase = None
lastclass = None
lasti = 0
for i in xrange(len(val) + 1):
# this extra is being used to handle the case when
# a sequence is all bases
if i < len(val):
base = val[i]
else:
base = '-'
if base not in baseclasses:
baseclass = NOBASE
else:
baseclass = baseclasses[base]
if baseclass == lastclass:
continue
if lastbase != None and lastclass == selectedClass:
boxpts.extend([
lasti, -row, lasti, -row - 1, i, -row - 1, i, -row
])
diagpts.extend([i, -row, i, -row - 1])
#diagpts.extend([lasti, -row, i, -row-1])
#diagpts2.extend([lasti, -row, lasti, -row-1])
lasti = i
lastbase = base
lastclass = baseclass
return boxpts, diagpts, diagpts2
base_boxpts, base_diagpts, base_diagpts2 = getRegions(BASE)
nobase_boxpts, nobase_diagpts, nobase_diagpts2 = getRegions(NOBASE)
# build labels
if self.show_labels:
labels = []
for i, key in zip(self.rowspacing, self.aln):
labels.append(
text_clip(key, -util.INF, -i, 0, -i - 1, 4, 12, "middle",
"right"))
labelsgroup = group(*labels)
else:
labelsgroup = group()
# build hotspot
click = hotspot("click", 0, 0, self.aln.alignlen(), -self.size[1],
self.on_click_callback)
self.text_group = group()
return group(
translate(
self.pos[0],
self.pos[1] + self.size[1],
color(0, 0, 0),
labelsgroup,
click,
color(.5, .5, .5),
quads(*base_boxpts),
lines(*base_diagpts),
#lines(* base_diagpts2),
color(.7, .2, .2),
quads(*nobase_boxpts),
lines(*nobase_diagpts),
#lines(* nobase_diagpts2),
group(self.text_group)))
def draw_left(self):
labels = []
maxsize = max(map(len, self.aln.keys()))
for i, key in enumerate(self.aln):
labels.append(
text_clip(key, -util.INF, -i, 0, -i - 1, 4, 12, "middle",
"right"))
return group(
translate(
self.pos[0],
self.pos[1] + self.size[1],
color(0, 0, 0),
#lines(0, 0, 0, -len(self.aln),
# -maxsize, 0, 0, 0,
# -maxsize, -len(self.aln), 0, -len(self.aln)),
*labels))
def update(self):
win = self.get_window()
view = win.get_visible()
size = win.get_size()
x, y = self.pos
mintextSize = 4
minblockSize = 1
color_bases = self.color_bases
if self.multiscale.atleast(minblockSize, .1, view=view, size=size):
if not self.text_shown or \
not self.multiscale.same_view(view):
self.text_shown = True
start = max(int(self.multiscale.worldx1 - x - 1), 0)
end = max(int(self.multiscale.worldx2 - x), start)
vis = []
vis2 = []
for i, row in enumerate(self.aln.itervalues()):
seq = row[start:end]
seq = seq.replace("-", " ")
# color bases
if self.show_color_bases and color_bases != False:
for j in xrange(len(seq)):
base = seq[j].upper()
if base in color_bases:
vis2.extend([
color_bases[base],
quads(start + j, -i, start + j, -i - 1,
start + j + 1, -i - 1, start + j + 1,
-i)
])
end2 = start + len(seq)
# draw text
if self.show_bases and \
self.multiscale.atleast(mintextSize, 2,
view=view, size=size):
vis.append(
text_scale(seq, start, -i + 1, end2, -i - 1,
"left", "bottom"))
self.text_group = win.replace_group(
self.text_group, group(group(*vis2), color(0, 0, 0), *vis))
elif self.text_shown:
self.text_shown = False
self.text_group = win.replace_group(self.text_group, group())
def on_click_callback(self):
# TODO: should not rely on get_mouse_pos("world")
win = self.get_window()
x, y = win.get_mouse_pos('world')
x -= self.pos[0]
y = self.size[1] - (y - self.pos[1])
self.on_click(x, y)
def on_click(self, x, y):
y = int(y)
if 0 <= y < len(self.aln):
print self.aln.keys()[y]
