def getCoverFeature(self):
total = 0
nameParts = []
for w in self.words:
count = sum([1 for b in self.getBeds(w)])
total+=count
nameParts.append(w+"="+str(count))
b = bed.Feature(self.chrom, self.start, self.end, "_".join(nameParts), total, "+")
return b
def getBeds(self, word):
start = int(self.start)
wordCount = len(self.words.get(word,[]))
for p in self.words.get(word, []):
if p == "":
break
#pos, strand = p.split("/")
pos, strand = p
pos = int(pos)
yield(bed.Feature(self.chrom, start+pos, start+pos+len(word), word, wordCount, strand))
def getBedFeature(self):
b = bed.Feature(seqid=self.chrom, start=self.start, end=self.end, score=self.score)
return b