def overlaps(hits, fasta_index, backtrans=False):
tree = IntervalTree()
faidx = fasta.Indexer("", fasta_index)
faidx.load()
prevOrg, curOrg = None, None
prevStrand, curStrand = None, None
newHits = []
# print "Before",len(hits)
for hit in hits:
acc, clrname, full_evalue, hmm_st, hmm_end, env_st, env_end, description = hit[:8]
curOrg = fasta.getName(acc)
if backtrans:
hitSt, curStrand = faidx.sixframe_to_nucleotide(acc, env_st)
hitEnd, curStrand = faidx.sixframe_to_nucleotide(acc, env_end)
else:
hitSt, hitEnd = map(int, [env_st, env_end])
if prevOrg == None:
prevOrg = curOrg
prevStrand = curStrand
tree.add(hitSt, hitEnd, hit)
newHits.append(hit)
elif prevOrg != curOrg or prevStrand != curStrand:
tree = IntervalTree()
tree.add(hitSt, hitEnd, hit)
prevOrg = curOrg
prevStrand = curStrand
newHits.append(hit)
else:
overlaps = tree.find(hitSt, hitEnd)
if len(overlaps) == 0:
tree.add(hitSt, hitEnd, hit)
newHits.append(hit)
# print "After",len(newHits)
return newHits
def unique(hits):
hitset = set()
newHits = []
for hit in hits:
acc, clrname, full_evalue, hmm_st, hmm_end, env_st, env_end, description = hit[:8]
curOrg = fasta.getName(acc)
if (env_st, env_end, curOrg) in hitset:
continue
hitset.add((env_st, env_end, curOrg))
newHits.append(hit)
return newHits
