TST: Ensure current parsers create MultiDiGraphs

... even though the fastg / gfa ones don't actually allow for parallel
edges in parsing (marbl#239). We just wanna *create* a multidigraph so that
in the later stages of pattern identification, etc. (marbl#202), we can
assume safely that the object we are working with is a multidigraph.

metagenomescope/tests/assembly_graph_parser/test_parse_fastg.py

@@ -1,3 +1,4 @@
+import networkx as nx
 from .utils import run_tempfile_test
 
 
@@ -24,6 +25,7 @@ def get_test_fastg():
 
 def test_good():
     g = run_tempfile_test("fastg", get_test_fastg(), None, None)
+    assert type(g) is nx.MultiDiGraph
     # CODELINK: remaining code in this function is taken from
     # test_parse_small_assembly_graph() in the pyfastg codebase.
     # (...I mean, I literally wrote that function, but might as well cite it?)

metagenomescope/tests/assembly_graph_parser/test_parse_gfa.py

@@ -1,4 +1,4 @@
-# from .utils import run_tempfile_test
+import networkx as nx
 from metagenomescope.input_node_utils import negate_node_id
 from metagenomescope.assembly_graph_parser import parse_gfa
 from metagenomescope.errors import GraphParsingError
@@ -8,7 +8,7 @@
 
 def check_sample_gfa_digraph(digraph):
     """Checks that all of the collected data (nodes, edges, node gc content)
-    looks good for the NX DiGraph produced by running parse_gfa() on
+    looks good for the NX MultiDiGraph produced by running parse_gfa() on
     sample1.gfa or sample2.gfa.
 
     (sample1.gfa and sample2.gfa describe the same graph structure, albeit in
@@ -19,6 +19,7 @@ def check_sample_gfa_digraph(digraph):
     the ways parse_gfa() cares about), and 2) it lets me be lazy and reuse all
     of this test code ;)
     """
+    assert type(digraph) is nx.MultiDiGraph
     assert len(digraph.nodes) == 12
     assert len(digraph.edges) == 8
 
@@ -82,12 +83,11 @@ def test_parse_self_implied_edge():
     We define a "self-implied edge" as an edge whose complement is itself. An
     example of such an edge is 2+ -> 2- in loop.gfa; the complement of this
     edge is -(2-) -> -(2+), which is equal to 2+ -> 2- (my notation looks kind
-    of sillyt but you get the idea).
+    of silly but you get the idea).
 
     The expected behavior is that self-implied edges are only added to the
-    assembly graph visualization once, since duplicate edges in general don't
-    really make sense here. This corroborates the visualization of loop.gfa in
-    Shaun's repository containing it
+    assembly graph visualization once. This corroborates the visualization of
+    loop.gfa in Shaun's repository containing it
     (https://github.com/sjackman/assembly-graph).
     """
     digraph = parse_gfa("metagenomescope/tests/input/loop.gfa")

metagenomescope/tests/assembly_graph_parser/test_parse_lastgraph.py

@@ -1,3 +1,4 @@
+import networkx as nx
 from .utils import run_tempfile_test
 from metagenomescope.errors import GraphParsingError
 from metagenomescope.assembly_graph_parser import parse_lastgraph
@@ -10,7 +11,9 @@ def test_parse_lastgraph_good():
     digraph = parse_lastgraph(
         "metagenomescope/tests/input/cycletest_LastGraph"
     )
-    # Verify that a NetworkX DiGraph was computed based on this file accurately
+    # Verify that a NetworkX MultiDiGraph was computed based on this file
+    # accurately.
+    assert type(digraph) is nx.MultiDiGraph
     # We expect 4 nodes and 4 edges due to the graph being interpreted as
     # unoriented (i.e. each node's forward or reverse orientation can be used)
     assert len(digraph.nodes) == 4
@@ -44,10 +47,11 @@ def test_parse_lastgraph_good():
     assert digraph.nodes["-2"]["gc_content"] == (1 / 6)
 
     # Check that edges were properly stored in the digraph
-    for edge_id in (("1", "2"), ("-2", "-1")):
+    # (The 0s correspond to keys, since this is a multigraph)
+    for edge_id in (("1", "2", 0), ("-2", "-1", 0)):
         assert edge_id in digraph.edges
         assert digraph.edges[edge_id]["multiplicity"] == 5
-    for edge_id in (("2", "1"), ("-1", "-2")):
+    for edge_id in (("2", "1", 0), ("-1", "-2", 0)):
         assert edge_id in digraph.edges
         assert digraph.edges[edge_id]["multiplicity"] == 9
 

metagenomescope/tests/assembly_graph_parser/test_parse_metacarvel_gml.py

@@ -1,3 +1,4 @@
+import networkx as nx
 from networkx import NetworkXError
 from .utils import run_tempfile_test
 from metagenomescope.errors import GraphParsingError
@@ -20,6 +21,7 @@ def test_parse_metacarvel_gml_good():
     digraph = parse_metacarvel_gml(
         "metagenomescope/tests/input/marygold_fig2a.gml"
     )
+    assert type(digraph) is nx.MultiDiGraph
     # Make sure that the appropriate amounts of nodes and edges are read
     assert len(digraph.nodes) == 12
     assert len(digraph.edges) == 16