def test_extend_bug(self):
cluster = Cluster(read=BED, write=PK)
cluster.read_line('chr3 1 35 666 noname +')
cluster2 = Cluster(read=BED, write=PK)
cluster2.read_line('chr3 156 200 666 noname -')
cluster.extend(100)
cluster2.extend(100)
result = cluster + cluster2
self.assertEqual(200, len(result))
def test_extend(self):
cluster = Cluster(read=BED)
cluster.read_line('chr3 1 35 noname 666 +')
cluster2 = Cluster(read=BED)
cluster2.read_line('chr3 56 100 noname 666 -')
cluster.extend(100)
cluster2.extend(100)
self.assertEqual(cluster.write_line(), 'chr3\t1\t100\t100:1.00\t1.0\t+\t50\t100.0\n')
self.assertEqual(cluster2.write_line(), 'chr3\t1\t100\t100:1.00\t1.0\t-\t50\t100.0\n')
def read_and_extend(self, cluster, line, extension):
cluster_aux = Cluster(read=BED, write=BED, read_half_open=True, write_half_open=True, rounding = True)
if cluster.is_empty():
cluster.read_line(line)
cluster.extend(extension)
#print cluster.write_line(), cluster._profile
else:
cluster_aux.read_line(line)
cluster_aux.extend(extension)
#print cluster_aux.write_line(), cluster_aux._profile
cluster += cluster_aux
#print cluster.write_line()
return cluster
def test_bed_half_open_to_wig_half_open2(self):
cluster = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding=True, cached=True)
cluster2 = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding=True, cached=True)
cluster3 = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding=True, cached=True)
result = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding=True)
extension = 130
result.read_line('chr1 156 192 id:7043691 1000 +')
result.extend(extension)
cluster.read_line('chr1 241 277 id:916714 1000 +')
cluster.extend(extension)
result +=cluster
cluster2.read_line('chr1 241 277 id:916714 1000 +')
cluster2.extend(extension)
result +=cluster2
cluster3.read_line('chr1 241 277 id:6880101 1000 +')
cluster3.extend(extension)
result +=cluster3
self.assertEqual(result.write_line(), 'chr1\t156\t241\t1\nchr1\t241\t286\t4\nchr1\t286\t371\t3\n')
