def add(self,region):
"""Add a new Region-like object to the RegionList"""
try:
self[region.chromosome].insert(region.rbeg,region.rend,region)
except KeyError:
itree = IntervalTree()
itree.insert(region.rbeg,region.rend,region)
self[region.chromosome]=itree
def btab_reclist_to_interval_list_0basedStart(recs):
"""
Return chr, list of IntervalNode
"""
tree = IntervalTree()
for rec in recs:
tree.insert(rec['rStart1'] - 1, rec['rEnd1'])
path = []
tree.traverse(path.append)
chr = recs[0]['chr']
return chr, path
def btab_reclist_to_interval_list_0basedStart(recs):
"""
Return chr, list of IntervalNode
"""
tree = IntervalTree()
for rec in recs:
tree.insert(rec['rStart1']-1, rec['rEnd1'])
path = []
tree.traverse(path.append)
chr = recs[0]['chr']
return chr, path
def btab_reclist_to_interval_list_0basedStart(recs):
"""
Return chr, list of IntervalNode
"""
tree = IntervalTree()
for rec in recs:
tree.insert(rec["rStart1"] - 1, rec["rEnd1"])
path = []
tree.traverse(path.append)
seqname = recs[0]["chr"]
return seqname, path
def setUp(self):
iv = IntervalTree()
n = 0
for i in range(1, 1000, 80):
iv.insert(i, i + 10, dict(value=i * i))
# add is synonym for insert.
iv.add(i + 20, i + 30, dict(astr=str(i * i)))
# or insert/add an interval object with start, end attrs.
iv.insert_interval(
Interval(i + 40, i + 50, value=dict(astr=str(i * i))))
iv.add_interval(
Interval(i + 60, i + 70, value=dict(astr=str(i * i))))
n += 4
self.intervals = self.iv = iv
self.nintervals = n
def setUp(self):
iv = IntervalTree()
n = 0
for i in range(1, 1000, 80):
iv.insert(i, i + 10, dict(value=i*i))
# add is synonym for insert.
iv.add(i + 20, i + 30, dict(astr=str(i*i)))
# or insert/add an interval object with start, end attrs.
iv.insert_interval(Interval(i + 40, i + 50,
value=dict(astr=str(i*i))))
iv.add_interval(Interval(i + 60, i + 70,
value=dict(astr=str(i*i))))
n += 4
self.intervals = self.iv = iv
self.nintervals = n
def add_new_locus(match, overlappers, chromo):
intersecter = IntervalTree()
locus = match.name2.split('|')[1]
intersecter.insert(match.zstart1, match.end1, locus)
overlappers[chromo][locus] = intersecter
return overlappers
def add_new_locus(match, overlappers, chromo):
intersecter = IntervalTree()
locus = match.name2.split('|')[1]
intersecter.insert(match.zstart1, match.end1, locus)
overlappers[chromo][locus] = intersecter
return overlappers
