def print_gene(self, gene):
print "%s %s:%s:%s-%s (%s)" % (
gene.data["ID"], gene.species, gene.seqname,
util.int2pretty(gene.start), util.int2pretty(
gene.end), util.int2pretty(gene.length()))
print ";".join("%s=%s" % (a, b) for a, b in gene.data.items())
print
def print_gene(self, gene):
print "%s %s:%s:%s-%s (%s)" % (
gene.data["ID"], gene.species,
gene.seqname,
util.int2pretty(gene.start),
util.int2pretty(gene.end),
util.int2pretty(gene.length()))
print ";".join("%s=%s" % (a, b) for a,b in gene.data.items())
print
def frag_click(self, frag):
x, y = self.win.get_mouse_pos("world")
if frag.direction == 1:
pos = int(frag.start + x - frag.x)
else:
pos = int(frag.end - (x - frag.x))
print "%s:%s:%s" % (frag.genome, frag.chrom, util.int2pretty(pos))
def frag_click(self, frag):
x, y = self.win.get_mouse_pos("world")
if frag.direction == 1:
pos = int(frag.start + x - frag.x)
else:
pos = int(frag.end - (x - frag.x))
print "%s:%s:%s" % (frag.genome, frag.chrom,
util.int2pretty(pos))
def on_click(self, clickx, clicky):
# determine regions that have been clicked
self.selgenes1 = self.get_regions_by_pos(self.layout1, clickx)
self.selgenes2 = self.get_regions_by_pos(self.layout2, clicky)
print
for gene in self.selgenes1:
if "ID" not in gene.data:
continue
print "X %10s (%s %s:%s-%s)" % (
gene.data["ID"], gene.species, gene.seqname,
util.int2pretty(gene.start), util.int2pretty(gene.end))
for gene in self.selgenes2:
if "ID" not in gene.data:
continue
print "Y %10s (%s %s:%s-%s)" % (
gene.data["ID"], gene.species, gene.seqname,
util.int2pretty(gene.start), util.int2pretty(gene.end))
def on_select(self, pos1, pos2):
"""Callback for region selections"""
# determine selected chrom
chrom = self.pos2chrom(*pos1)
chrom2 = self.pos2chrom(*pos2)
if chrom == None:
print "no chromosome selected"
return
if chrom != chrom2:
print "please select only one chromosome"
return
x1 = pos1[0]
x2 = pos2[0]
if x1 > x2:
x1, x2 = x2, x1
chrom_pos = self.chrom_pos[chrom][0]
newchrom = Region(chrom.species, chrom.seqname, chrom.feature,
int(max(chrom.start + x1 - chrom_pos, 0)),
int(min(chrom.start + x2 - chrom_pos, chrom.end)))
print "displaying region: %s:%s:%s-%s:%s" % \
(newchrom.species, newchrom.seqname,
util.int2pretty(newchrom.start),
util.int2pretty(newchrom.end),
["+", "+", "-"][newchrom.strand])
# create sub-browser
subbrowser = GenomeOverview([newchrom],
winpos=self.win.get_position(),
winsize=self.win.get_size())
for track_class, offset, args, kargs, tracks in self.metatracks:
subbrowser.add_track(track_class, offset, *args, **kargs)
subbrowser.show()
def on_select(self, pos1, pos2):
"""Callback for region selections"""
# determine selected chrom
chrom = self.pos2chrom(*pos1)
chrom2 = self.pos2chrom(*pos2)
if chrom == None:
print "no chromosome selected"
return
if chrom != chrom2:
print "please select only one chromosome"
return
x1 = pos1[0]
x2 = pos2[0]
if x1 > x2:
x1, x2 = x2, x1
chrom_pos = self.chrom_pos[chrom][0]
newchrom = Region(chrom.species, chrom.seqname, chrom.feature,
int(max(chrom.start + x1 - chrom_pos, 0)),
int(min(chrom.start + x2 - chrom_pos, chrom.end)))
print "displaying region: %s:%s:%s-%s:%s" % \
(newchrom.species, newchrom.seqname,
util.int2pretty(newchrom.start),
util.int2pretty(newchrom.end),
["+", "+", "-"][newchrom.strand])
# create sub-browser
subbrowser = GenomeOverview([newchrom],
winpos=self.win.get_position(),
winsize=self.win.get_size())
for track_class, offset, args, kargs, tracks in self.metatracks:
subbrowser.add_track(track_class, offset, *args, **kargs)
subbrowser.show()
def on_click(self, clickx, clicky):
# determine regions that have been clicked
self.selgenes1 = self.get_regions_by_pos(self.layout1, clickx)
self.selgenes2 = self.get_regions_by_pos(self.layout2, clicky)
print
for gene in self.selgenes1:
if "ID" not in gene.data:
continue
print "X %10s (%s %s:%s-%s)" % (gene.data["ID"],
gene.species,
gene.seqname,
util.int2pretty(gene.start),
util.int2pretty(gene.end))
for gene in self.selgenes2:
if "ID" not in gene.data:
continue
print "Y %10s (%s %s:%s-%s)" % (gene.data["ID"],
gene.species,
gene.seqname,
util.int2pretty(gene.start),
util.int2pretty(gene.end))
def func():
x, y = win.get_mouse_pos()
print "pos=%s age=%f" % (util.int2pretty(int(x)), y)
def func():
x, y = win.get_mouse_pos()
print "pos=%s age=%f" % (util.int2pretty(int(x)), y)
def test_pretty_int(self):
self.assertEqual(util.int2pretty(0), '0')
self.assertEqual(util.int2pretty(1), '1')
self.assertEqual(util.int2pretty(10), '10')
self.assertEqual(util.int2pretty(100), '100')
self.assertEqual(util.int2pretty(1000), '1,000')
self.assertEqual(util.int2pretty(10000), '10,000')
self.assertEqual(util.int2pretty(100000), '100,000')
self.assertEqual(util.int2pretty(1000000), '1,000,000')
self.assertEqual(util.int2pretty(-1), '-1')
self.assertEqual(util.int2pretty(-10), '-10')
self.assertEqual(util.int2pretty(-100), '-100')
self.assertEqual(util.int2pretty(-1000), '-1,000')
self.assertEqual(util.int2pretty(-10000), '-10,000')
self.assertEqual(util.int2pretty(-100000), '-100,000')
self.assertEqual(util.int2pretty(-1000000), '-1,000,000')
self.assertEqual(util.pretty2int('0'), 0)
self.assertEqual(util.pretty2int('1'), 1)
self.assertEqual(util.pretty2int('10'), 10)
self.assertEqual(util.pretty2int('100'), 100)
self.assertEqual(util.pretty2int('1,000'), 1000)
self.assertEqual(util.pretty2int('10,000'), 10000)
self.assertEqual(util.pretty2int('100,000'), 100000)
self.assertEqual(util.pretty2int('1,000,000'), 1000000)
self.assertEqual(util.pretty2int('-1'), -1)
self.assertEqual(util.pretty2int('-10'), -10)
self.assertEqual(util.pretty2int('-100'), -100)
self.assertEqual(util.pretty2int('-1,000'), -1000)
self.assertEqual(util.pretty2int('-10,000'), -10000)
self.assertEqual(util.pretty2int('-100,000'), -100000)
self.assertEqual(util.pretty2int('-1,000,000'), -1000000)
def test_pretty_int(self):
self.assertEqual(util.int2pretty(0), "0")
self.assertEqual(util.int2pretty(1), "1")
self.assertEqual(util.int2pretty(10), "10")
self.assertEqual(util.int2pretty(100), "100")
self.assertEqual(util.int2pretty(1000), "1,000")
self.assertEqual(util.int2pretty(10000), "10,000")
self.assertEqual(util.int2pretty(100000), "100,000")
self.assertEqual(util.int2pretty(1000000), "1,000,000")
self.assertEqual(util.int2pretty(-1), "-1")
self.assertEqual(util.int2pretty(-10), "-10")
self.assertEqual(util.int2pretty(-100), "-100")
self.assertEqual(util.int2pretty(-1000), "-1,000")
self.assertEqual(util.int2pretty(-10000), "-10,000")
self.assertEqual(util.int2pretty(-100000), "-100,000")
self.assertEqual(util.int2pretty(-1000000), "-1,000,000")
self.assertEqual(util.pretty2int("0"), 0)
self.assertEqual(util.pretty2int("1"), 1)
self.assertEqual(util.pretty2int("10"), 10)
self.assertEqual(util.pretty2int("100"), 100)
self.assertEqual(util.pretty2int("1,000"), 1000)
self.assertEqual(util.pretty2int("10,000"), 10000)
self.assertEqual(util.pretty2int("100,000"), 100000)
self.assertEqual(util.pretty2int("1,000,000"), 1000000)
self.assertEqual(util.pretty2int("-1"), -1)
self.assertEqual(util.pretty2int("-10"), -10)
self.assertEqual(util.pretty2int("-100"), -100)
self.assertEqual(util.pretty2int("-1,000"), -1000)
self.assertEqual(util.pretty2int("-10,000"), -10000)
self.assertEqual(util.pretty2int("-100,000"), -100000)
self.assertEqual(util.pretty2int("-1,000,000"), -1000000)
