def setup_method(self, method):
self.rmt = RegionMatrixTable(
additional_edge_fields={
'weight': tables.Int32Col(pos=0),
'foo': tables.Int32Col(pos=1),
'bar': tables.Float32Col(pos=2),
'baz': tables.StringCol(50, pos=3)
})
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 = GenomicRegion(chromosome=chromosome, start=start, end=end)
self.rmt.add_region(node)
self.rmt.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.rmt.add_edge(edge)
self.rmt.flush()
def test_add_edge(self):
rmt = self.rp_class(
additional_edge_fields={'weight': tables.Float64Col()})
rmt.add_region(GenomicRegion(chromosome='1', start=1, end=1000))
rmt.flush()
rmt.add_edge(Edge(0, 0, weight=100))
rmt.flush()
edge = rmt.edges[0]
assert edge.source == 0
assert edge.sink == 0
assert edge.weight == 100
rmt.close()
rmt = self.rp_class(
additional_edge_fields={'weight': tables.Float64Col()})
rmt.add_region(GenomicRegion(chromosome='1', start=1, end=1000))
rmt.flush()
rmt.add_edge_simple(0, 0, 100)
rmt.flush()
edge = rmt.edges[0]
assert edge.source == 0
assert edge.sink == 0
assert edge.weight == 100
rmt.close()
rmt = self.rp_class(
additional_edge_fields={'weight': tables.Float64Col()})
rmt.add_region(GenomicRegion(chromosome='1', start=1, end=1000))
rmt.flush()
rmt.add_edge({'source': 0, 'sink': 0, 'weight': 100})
rmt.flush()
edge = rmt.edges[0]
assert edge.source == 0
assert edge.sink == 0
assert edge.weight == 100
rmt.close()
def sample_hic(file_name=None, tmpdir=None):
hic = Hic(file_name=file_name, tmpdir=tmpdir, mode='w')
# add some nodes (12 to be exact)
nodes = []
for i in range(1, 5000, 1000):
nodes.append(GenomicRegion(chromosome="chr1", start=i, end=i+1000-1))
for i in range(1, 3000, 1000):
nodes.append(GenomicRegion(chromosome="chr2", start=i, end=i+1000-1))
for i in range(1, 2000, 500):
nodes.append(GenomicRegion(chromosome="chr3", start=i, end=i+1000-1))
hic.add_regions(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)
return hic
def sample_hic_matrix2(file_name=None, tmpdir=None):
# 0 1 2 3 4 5 6 7 8 9
# #####################
# 0 # 0 1 0 2 - 3 0 - 0 5
# 1 # 6 0 7 - 8 0 - 0 1
# 2 # 2 3 - 0 5 - 0 6
# 3 # 7 - 8 9 - 1 0
# 4 # - - - - - -
# 5 # 5 6 - 8 9
# 6 # 1 - 0 0
# 7 # - - -
# 8 # 0 4
# 9 # 5
nodes = [
GenomicRegion('chr1', 1, 1000),
GenomicRegion('chr1', 1001, 2000),
GenomicRegion('chr1', 2001, 3000),
GenomicRegion('chr1', 3001, 4000),
GenomicRegion('chr1', 4001, 5000),
GenomicRegion('chr1', 5001, 6000),
GenomicRegion('chr1', 6001, 7000),
GenomicRegion('chr1', 7001, 8000),
GenomicRegion('chr1', 8001, 9000),
GenomicRegion('chr1', 9001, 10000)
]
edges = [
Edge(source=0, sink=1, weight=1), Edge(source=3, sink=5, weight=8),
Edge(source=0, sink=3, weight=2), Edge(source=3, sink=6, weight=9),
Edge(source=0, sink=5, weight=3), Edge(source=3, sink=8, weight=1),
Edge(source=0, sink=9, weight=5),
Edge(source=1, sink=1, weight=6),
Edge(source=1, sink=3, weight=7), Edge(source=5, sink=5, weight=5),
Edge(source=1, sink=5, weight=8), Edge(source=5, sink=6, weight=6),
Edge(source=1, sink=9, weight=1), Edge(source=5, sink=8, weight=8),
Edge(source=2, sink=2, weight=2), Edge(source=5, sink=9, weight=9),
Edge(source=2, sink=3, weight=3), Edge(source=6, sink=6, weight=1),
Edge(source=2, sink=6, weight=5),
Edge(source=2, sink=9, weight=6), Edge(source=8, sink=9, weight=4),
Edge(source=3, sink=3, weight=7), Edge(source=9, sink=9, weight=5)
]
hic = Hic(file_name=file_name, tmpdir=tmpdir)
hic.add_regions(nodes)
hic.add_edges(edges)
return hic
def sample_hic_matrix1(file_name=None, tmpdir=None):
# 0 1 2 3 4 5 6 7 8 9
# #####################
# 0 # 0 1 0 2 0 3 0 4 0 5
# 1 # 6 0 7 0 8 0 9 0 1
# 2 # 2 3 4 0 5 0 0 6
# 3 # 7 0 8 9 0 1 0
# 4 # 0 2 3 0 0 4
# 5 # 5 6 7 8 9
# 6 # 1 0 0 0
# 7 # 2 3 0
# 8 # 0 4
# 9 # 5
nodes = [
GenomicRegion('chr1', 1, 1000),
GenomicRegion('chr1', 1001, 2000),
GenomicRegion('chr1', 2001, 3000),
GenomicRegion('chr1', 3001, 4000),
GenomicRegion('chr1', 4001, 5000),
GenomicRegion('chr1', 5001, 6000),
GenomicRegion('chr1', 6001, 7000),
GenomicRegion('chr1', 7001, 8000),
GenomicRegion('chr1', 8001, 9000),
GenomicRegion('chr1', 9001, 10000)
]
edges = [
Edge(source=0, sink=1, weight=1), Edge(source=3, sink=5, weight=8),
Edge(source=0, sink=3, weight=2), Edge(source=3, sink=6, weight=9),
Edge(source=0, sink=5, weight=3), Edge(source=3, sink=8, weight=1),
Edge(source=0, sink=7, weight=4), Edge(source=4, sink=5, weight=2),
Edge(source=0, sink=9, weight=5), Edge(source=4, sink=6, weight=3),
Edge(source=1, sink=1, weight=6), Edge(source=4, sink=9, weight=4),
Edge(source=1, sink=3, weight=7), Edge(source=5, sink=5, weight=5),
Edge(source=1, sink=5, weight=8), Edge(source=5, sink=6, weight=6),
Edge(source=1, sink=7, weight=9), Edge(source=5, sink=7, weight=7),
Edge(source=1, sink=9, weight=1), Edge(source=5, sink=8, weight=8),
Edge(source=2, sink=2, weight=2), Edge(source=5, sink=9, weight=9),
Edge(source=2, sink=3, weight=3), Edge(source=6, sink=6, weight=1),
Edge(source=2, sink=4, weight=4), Edge(source=7, sink=7, weight=2),
Edge(source=2, sink=6, weight=5), Edge(source=7, sink=8, weight=3),
Edge(source=2, sink=9, weight=6), Edge(source=8, sink=9, weight=4),
Edge(source=3, sink=3, weight=7), Edge(source=9, sink=9, weight=5)
]
hic = Hic(file_name=file_name, tmpdir=tmpdir)
hic.add_regions(nodes)
hic.add_edges(edges)
return hic