def as_bed(self):
sc = SegmentChain(self.don, self.acc)
ts = sc.spanning_segment.start
te = sc.spanning_segment.end
b = sc.as_bed(thickstart=ts, thickend=te).strip("\n").split("\t")
b.extend(map(str, [self.nevi, self.ntot]))
return b
class JncGroup:
"""Junction Group"""
def __init__(self, js):
self.jsli = [js]
self.corejs = js
self.sc = SegmentChain(js.don, js.acc)
self.name = None
def distance2(self, js):
return max(self.corejs.dist2don(js), self.corejs.dist2acc(js))
def add(self, js):
self.jsli.append(js)
def merge(self):
for i in range(1, len(self.jsli)):
js = self.jsli[i]
self.sc.add_segments(js.don)
self.sc.add_segments(js.acc)
def get_ntot(self):
return sum(js.ntot for js in self.jsli)
def get_nevi(self):
return sum(js.nevi for js in self.jsli)
def set_name(self, name):
self.name = name
def as_bed(self):
if self.name is not None:
self.sc.attr['ID'] = self.name
if self.sc.strand == "+":
color = "255,0,0"
else:
color = "0,0,255"
self.sc.attr['color'] = color
b = self.sc.as_bed().strip("\n").split("\t")
b.extend(map(str, [self.get_nevi(), self.get_ntot()]))
return b
def __str__(self):
return "\t".join(
map(str,
[self.corejs, self.get_ntot(),
self.get_nevi()]))
def jncsites(self):
jncs = []
for i in range(len(self.jsli)):
jncs.append([self.name, str(i + 1)] + self.jsli[i].as_bed())
i += 1
return jncs