def read_entry(self):
# Find our current lowest range
output = []
for i in self.buffers:
output.append([])
rngs = [x.get_range() for x in self.buffers if x]
#print rngs
if len(rngs) == 0: return None
srngs = sorted(rngs, key=lambda x: (x.chr, x.start, x.end))
mrngs = merge_ranges(srngs)
current_range = mrngs[0]
#print current_range.get_range_string()
got_overlap = True
while got_overlap == True:
got_overlap = False
for i in range(0, len(self.buffers)):
if not self.buffers[i]: continue #end of this one
v = self.buffers[i].get_range().cmp(current_range)
if v == 0:
got_overlap = True
if self.buffers[i].get_range().overlaps(current_range):
current_range = current_range.merge(
self.buffers[i].get_range())
output[i].append(self.buffers[i])
self.buffers[i] = self.streams[i].read_entry()
#print str([len(x) for x in output])+"\t"+current_range.get_range_string()
#print str(i)+":"+str(v)
current_range.set_payload(output)
return current_range
def read_entry(self):
# Find our current lowest range
output = []
for i in self.buffers:
output.append([])
rngs = [x.get_range() for x in self.buffers if x]
# print rngs
if len(rngs) == 0:
return None
srngs = sorted(rngs, key=lambda x: (x.chr, x.start, x.end))
mrngs = merge_ranges(srngs)
current_range = mrngs[0]
# print current_range.get_range_string()
got_overlap = True
while got_overlap == True:
got_overlap = False
for i in range(0, len(self.buffers)):
if not self.buffers[i]:
continue # end of this one
v = self.buffers[i].get_range().cmp(current_range)
if v == 0:
got_overlap = True
if self.buffers[i].get_range().overlaps(current_range):
current_range = current_range.merge(self.buffers[i].get_range())
output[i].append(self.buffers[i])
self.buffers[i] = self.streams[i].read_entry()
# print str([len(x) for x in output])+"\t"+current_range.get_range_string()
# print str(i)+":"+str(v)
current_range.set_payload(output)
return current_range
def union(self,tx2): # keep direction and name of self
all = []
for rng1 in [x.rng for x in self.exons]:
for rng2 in [y.rng for y in tx2.exons]:
u = rng1.union(rng2)
if u: all.append(u)
if len(all) == 0: return None
rngs = merge_ranges(all)
tx = Transcript()
tx.set_exons_and_junctions_from_ranges(rngs)
tx._direction = self._direction
tx._transcript_name = self._transcript_name
tx._gene_name = self._gene_name
return tx
def union(self, tx2): # keep direction and name of self
self._initialize()
all = []
for rng1 in [x.rng for x in self.exons]:
for rng2 in [y.rng for y in tx2.exons]:
u = rng1.union(rng2)
if u: all.append(u)
if len(all) == 0: return None
rngs = merge_ranges(all)
tx = Transcript()
tx.set_exons_and_junctions_from_ranges(rngs)
tx._direction = self._direction
tx._transcript_name = self._transcript_name
tx._gene_name = self._gene_name
return tx