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