def test_component_sorting_simple():
ag = AssemblyGraph("metagenomescope/tests/input/sample1.gfa")
ag.hierarchically_identify_patterns()
wccs = ag.get_connected_components()
# Four ccs:
# 1. 1+, 2+, 3+, Chain of [4-, 5+] (the chain is counted as a single node
# in the decomposed digraph)
# 2. 1-, 2-, 3-, Chain of [5-, 4+]
# 3. 6+
# 4. 6-
# Components 1/2 and 3/4 have the same number of nodes/edges/patterns, so
# the precise ordering is arbitrary. We just check that the number of
# top-level nodes ("real" nodes or collapsed patterns, stored in the 0th
# position of each 3-tuple in wccs) is correct, and that the total numbers
# of "real" nodes and edges in the component (stored in the 1st and 2nd
# position of each 3-tuple) is also correct.
assert len(wccs) == 4
assert len(wccs[0][0]) == 4
assert wccs[0][1] == 5
assert wccs[0][2] == 4
assert len(wccs[1][0]) == 4
assert wccs[1][1] == 5
assert wccs[1][2] == 4
assert len(wccs[2][0]) == 1
assert wccs[2][1] == 1
assert wccs[2][2] == 0
assert len(wccs[3][0]) == 1
assert wccs[3][1] == 1
assert wccs[3][2] == 0
def test_component_sorting_ecoli_graph():
ag = AssemblyGraph("metagenomescope/tests/input/E_coli_LastGraph")
ag.hierarchically_identify_patterns()
wccs = ag.get_connected_components()
# Assert that the first component is the big ugly one that contains node 89
seen_89_in_largest_cc = False
for node_id in wccs[0][0]:
if not ag.is_pattern(node_id):
if ag.decomposed_digraph.nodes[node_id]["name"] == "89":
seen_89_in_largest_cc = True
break
else:
# Recursively go through all patterns until we find 89
pattern_queue = [node_id]
while len(pattern_queue) > 0:
pattern = pattern_queue.pop()
patt_obj = ag.id2pattern[pattern]
for child_node_id in patt_obj.node_ids:
if ag.is_pattern(child_node_id):
pattern_queue.append(child_node_id)
else:
if ag.digraph.nodes[child_node_id]["name"] == "89":
seen_89_in_largest_cc = True
break
if seen_89_in_largest_cc:
break
assert seen_89_in_largest_cc
# Assert that components in the 1-indexed range [6, 11] are all cyclic
# chains with a single node and edge (i.e. they are sorted before the
# other components with just a single node each). This is because these are
# more "important" than these other components, at least to us.
for wcc_tuple in wccs[5:11]:
wcc = wcc_tuple[0]
# Check that the component contains just 1 node at the top level (a
# cyclic chain pattern)...
assert len(wcc) == 1
# ... and just 1 "real" node in full (the one node within the cyclic
# chain)
assert wcc_tuple[1] == 1
# ... and just 1 edge
assert wcc_tuple[2] == 1
cyc_id = list(wcc)[0]
assert ag.is_pattern(cyc_id)
# This cyclic chain should contain one node and one edge (and no other
# patterns within itself).
assert ag.id2pattern[cyc_id].get_counts(ag) == [1, 1, 0]