def cluster_hits(hits, radius1, radius2=None, samedir=False):
"""
Cluster hits using windows
hits -- iterable of tuples (region1, region2, extra)
radius -- radius of window in query genome
radius2 -- radius of window in subject genome (default=radius)
samdir -- whether or not to require genes in same direction
hits must be sorted by query region species, chrom, and start
"""
# connected components set
comps = {}
for hit, syntenic in find_syntenic_neighbors(hits, radius1, radius2):
# get block of hit
block = comps.get(hit, None)
if block is None:
block = UnionFind([hit])
comps[hit] = block
# union block with syntenic hits
for hit2 in syntenic:
block2 = comps.get(hit2, None)
# check whether hits are in the same direction
if samedir and not samedir_hits(hit, hit2):
if hit2 not in comps:
comps[hit2] = UnionFind([hit2])
continue
if block2 is None:
comps[hit2] = block
block.add(hit2)
else:
block2.union(block)
# get the set of blocks
comps = set(b.root() for b in comps.itervalues())
return comps
def test_union_find(self):
set1 = UnionFind()
set2 = UnionFind()
set3 = UnionFind()
set1.add(1)
set1.add(2)
self.assertEqual(len(set1), 2)
self.assertTrue(1 in set1)
self.assertFalse(set1.has(-1))
set2.add(3)
set2.add(4)
set2.add(5)
self.assertEqual(len(set2), 3)
set3.add(5)
set3.add(6)
set3.add(7)
self.assertEqual(len(set3), 3)
self.assertFalse(set1.same(set2))
set1.union(set2)
self.assertTrue(set1.same(set2))
set1.union(set3)
self.assertTrue(set1.members(), set([1, 2, 3, 4, 5, 6, 7]))
self.assertTrue(len(set1), len(set2))
def test_union_find(self):
set1 = UnionFind()
set2 = UnionFind()
set3 = UnionFind()
set1.add(1)
set1.add(2)
self.assertEqual(len(set1), 2)
self.assertTrue(1 in set1)
self.assertFalse(set1.has(-1))
set2.add(3)
set2.add(4)
set2.add(5)
self.assertEqual(len(set2), 3)
set3.add(5)
set3.add(6)
set3.add(7)
self.assertEqual(len(set3), 3)
self.assertFalse(set1.same(set2))
set1.union(set2)
self.assertTrue(set1.same(set2))
set1.union(set3)
self.assertTrue(
set1.members(),
set([1, 2, 3, 4, 5, 6, 7]))
self.assertTrue(len(set1), len(set2))
