def setup_method(self, method):
# make TAD-like structures for testing
hic = Hic()
nodes = []
for i in range(1, 12000, 1000):
node = Node(chromosome="chr1", start=i, end=i + 1000 - 1)
nodes.append(node)
for i in range(1, 4000, 500):
node = Node(chromosome="chr2", start=i, end=i + 500 - 1)
nodes.append(node)
hic.add_nodes(nodes)
edges = []
for i in range(0, 5):
for j in range(i, 5):
edges.append(Edge(source=i, sink=j, weight=50))
for i in range(6, 12):
for j in range(i, 12):
edges.append(Edge(source=i, sink=j, weight=75))
for i in range(13, 18):
for j in range(i, 18):
edges.append(Edge(source=i, sink=j, weight=30))
for i in range(18, 20):
for j in range(i, 20):
edges.append(Edge(source=i, sink=j, weight=50))
hic.add_edges(edges)
self.hic = hic
def get_hic(max_random_offset=2.0, amplify=False):
hic = Hic()
# add some nodes (120 to be exact)
nodes = []
for i in range(1, 5000, 1000):
nodes.append(Node(chromosome="chr1", start=i,
end=i + 1000 - 1))
for i in range(1, 3000, 1000):
nodes.append(Node(chromosome="chr2", start=i,
end=i + 1000 - 1))
for i in range(1, 2000, 500):
nodes.append(Node(chromosome="chr3", start=i,
end=i + 1000 - 1))
hic.add_nodes(nodes)
# add some edges with increasing weight for testing
edges = []
weight = 1.0
for i in range(0, len(nodes)):
for j in range(i, len(nodes)):
if amplify and i > 7:
a = 10.0
else:
a = 1.0
edges.append(
Edge(source=i,
sink=j,
weight=a +
weight * max_random_offset * random.random()))
weight += 1.0
hic.add_edges(edges)
return hic
def setup_method(self, method):
hic = Hic()
# add some nodes (120 to be exact)
nodes = []
for i in range(1, 5000, 1000):
nodes.append(Node(chromosome="chr1", start=i, end=i + 1000 - 1))
for i in range(1, 3000, 1000):
nodes.append(Node(chromosome="chr2", start=i, end=i + 1000 - 1))
for i in range(1, 2000, 500):
nodes.append(Node(chromosome="chr3", start=i, end=i + 1000 - 1))
hic.add_nodes(nodes)
# add some edges with increasing weight for testing
edges = []
weight = 1
for i in range(0, len(nodes)):
for j in range(i, len(nodes)):
edges.append(Edge(source=i, sink=j, weight=weight))
weight += 1
hic.add_edges(edges)
self.hic = hic
def _calculate(self, *args, **kwargs):
for i in range(10):
if i < 5:
chromosome = 'chr1'
start = i*1000
end = (i+1)*1000
elif i < 8:
chromosome = 'chr2'
start = (i-5)*1000
end = (i+1-5)*1000
else:
chromosome = 'chr3'
start = (i-8)*1000
end = (i+1-8)*1000
node = Node(chromosome=chromosome, start=start, end=end)
self.add_region(node, flush=False)
self.flush()
for i in range(10):
for j in range(i, 10):
edge = Edge(source=i, sink=j, weight=i*j, foo=i, bar=j, baz='x' + str(i*j))
self.add_edge(edge, flush=False)
self.flush()