def test_simple_pattern_layout():
ag = AssemblyGraph("metagenomescope/tests/input/bubble_test.gml")
ag.scale_nodes()
ag.compute_node_dimensions()
ag.scale_edges()
ag.hierarchically_identify_patterns()
# This graph should contain just a single bubble. We're going to verify
# that laying it out works as expected.
assert len(ag.bubbles) == 1
p = ag.bubbles[0]
p.layout(ag)
def test_compute_node_dimensions_all_lengths_equal():
ag = AssemblyGraph("metagenomescope/tests/input/loop.gfa")
ag.scale_nodes()
ag.compute_node_dimensions()
default_area = config.MIN_NODE_AREA + (
0.5 * (config.MAX_NODE_AREA - config.MIN_NODE_AREA)
)
default_height = default_area ** config.MID_LONGSIDE_PROPORTION
default_width = default_area / default_height
# This double-checks that the defaults we expect here are computed
# properly. If the config values are updated that may break this, so feel
# free to comment this out if that happens to you.
assert default_area == 5.5
assert default_height == approx(3.115839)
assert default_width == approx(1.765174)
for node in ag.digraph.nodes:
assert ag.digraph.nodes[node]["height"] == default_height
assert ag.digraph.nodes[node]["width"] == default_width
def test_compute_node_dimensions():
ag = AssemblyGraph("metagenomescope/tests/input/sample1.gfa")
ag.scale_nodes()
ag.compute_node_dimensions()
def get_dims(rl, lp):
area = config.MIN_NODE_AREA + (
rl * (config.MAX_NODE_AREA - config.MIN_NODE_AREA)
)
hgt = area ** lp
wid = area / hgt
return (wid, hgt)
# Relative length and longside proportions reused from test_scale_nodes()
nodename2dims = {
"1": get_dims(0.4180047, config.MID_LONGSIDE_PROPORTION),
"2": get_dims(0.5525722, config.HIGH_LONGSIDE_PROPORTION),
"3": get_dims(1, config.HIGH_LONGSIDE_PROPORTION),
"4": get_dims(0.3374782, config.MID_LONGSIDE_PROPORTION),
"5": get_dims(0.4180047, config.MID_LONGSIDE_PROPORTION),
"6": get_dims(0, config.LOW_LONGSIDE_PROPORTION),
}
seen_nodenames = []
for node in ag.digraph.nodes:
name = ag.digraph.nodes[node]["name"]
w = ag.digraph.nodes[node]["width"]
h = ag.digraph.nodes[node]["height"]
exp_data = ()
if name in nodename2dims:
exp_data = nodename2dims[name]
else:
exp_data = nodename2dims[negate_node_id(name)]
assert w == approx(exp_data[0])
assert h == approx(exp_data[1])
seen_nodenames.append(name)
assert len(seen_nodenames) == 12
def test_compute_node_dimensions_fails_if_scale_nodes_not_called_first():
# (Since relative_length and longside_proportion data won't be available.)
ag = AssemblyGraph("metagenomescope/tests/input/loop.gfa")
with raises(KeyError):
ag.compute_node_dimensions()
