ENH: first-pass LJA+Flye DOT parser; custom errors

needs testing, and this will crash downstream b/c the layout code/etc
expects nodes to have lengths. But overall, this is a good start.

from there -- need to allow other parsers to create multidigraphs (not
just this one) -- marbl#202. and, for DOT graphs, draw nodes as circles w/
uniform sizes (marbl#211). once these (and the requisite other hurdles i
haven't thought of r/n) are passed, we've got something going.

metagenomescope/errors.py

@@ -0,0 +1,2 @@
+class GraphParsingError(Exception):
+    pass

metagenomescope/tests/assembly_graph_parser/test_auxiliary_functions.py

@@ -76,6 +76,11 @@ def test_sniff_filetype():
     assert sniff_filetype("aSdF.FaStG") == "fastg"
     assert sniff_filetype("LastGraphfastg") == "fastg"
 
+    assert sniff_filetype("asdf.dot") == "dot"
+    assert sniff_filetype("ASDF.DOT") == "dot"
+    assert sniff_filetype("asdf.gv") == "gv"
+    assert sniff_filetype("ASDF.GV") == "gv"
+
     with pytest.raises(NotImplementedError):
         sniff_filetype("asdf.asdf")
     with pytest.raises(NotImplementedError):

metagenomescope/tests/assembly_graph_parser/test_parse_gfa.py

@@ -1,6 +1,7 @@
 # from .utils import run_tempfile_test
 from metagenomescope.input_node_utils import negate_node_id
 from metagenomescope.assembly_graph_parser import parse_gfa
+from metagenomescope.errors import GraphParsingError
 from .utils import run_tempfile_test
 from gfapy.error import InconsistencyError
 
@@ -134,7 +135,7 @@ def test_parse_no_length_node():
     s1.pop(1)
     s1.insert(1, "S\t1\t*")
     run_tempfile_test(
-        "gfa", s1, ValueError, "Found a node without a specified length: 1"
+        "gfa", s1, GraphParsingError, "Found a node without a specified length: 1"
     )
 
     # Manually assigning node 1 a sequence should fix the problem
@@ -177,7 +178,7 @@ def test_parse_invalid_id_node():
     run_tempfile_test(
         "gfa",
         s1,
-        ValueError,
+        GraphParsingError,
         "Node IDs in the input assembly graph cannot "
         'start with the "-" character.',
     )

metagenomescope/tests/assembly_graph_parser/test_parse_lastgraph.py

@@ -1,4 +1,5 @@
 from .utils import run_tempfile_test
+from metagenomescope.errors import GraphParsingError
 from metagenomescope.assembly_graph_parser import parse_lastgraph
 from metagenomescope.tests.assembly_graph_parser.test_validate_lastgraph import (
     reset_glines,
@@ -64,13 +65,13 @@ def test_parse_lastgraph_node_interrupted():
     glines = reset_glines()
     glines.pop(3)
     run_tempfile_test(
-        "LastGraph", glines, ValueError, "Line 4: Node block ends too early."
+        "LastGraph", glines, GraphParsingError, "Line 4: Node block ends too early."
     )
 
     glines = reset_glines()
     glines[2] = "ARC\t1\t1\t5"
     run_tempfile_test(
-        "LastGraph", glines, ValueError, "Line 3: Node block ends too early."
+        "LastGraph", glines, GraphParsingError, "Line 3: Node block ends too early."
     )
 
 
@@ -79,22 +80,22 @@ def test_parse_lastgraph_invalid_node_count():
     exp_msg = "Line 1: $NUMBER_OF_NODES must be a positive integer"
 
     glines[0] = "3.5\t10\t1\t1"
-    run_tempfile_test("LastGraph", glines, ValueError, exp_msg)
+    run_tempfile_test("LastGraph", glines, GraphParsingError, exp_msg)
 
     glines[0] = "-3.5\t10\t1\t1"
-    run_tempfile_test("LastGraph", glines, ValueError, exp_msg)
+    run_tempfile_test("LastGraph", glines, GraphParsingError, exp_msg)
 
     glines[0] = "-2\t10\t1\t1"
-    run_tempfile_test("LastGraph", glines, ValueError, exp_msg)
+    run_tempfile_test("LastGraph", glines, GraphParsingError, exp_msg)
 
     glines[0] = "2.0\t10\t1\t1"
-    run_tempfile_test("LastGraph", glines, ValueError, exp_msg)
+    run_tempfile_test("LastGraph", glines, GraphParsingError, exp_msg)
 
     glines[0] = "ABC\t10\t1\t1"
-    run_tempfile_test("LastGraph", glines, ValueError, exp_msg)
+    run_tempfile_test("LastGraph", glines, GraphParsingError, exp_msg)
 
     glines[0] = "0x123\t10\t1\t1"
-    run_tempfile_test("LastGraph", glines, ValueError, exp_msg)
+    run_tempfile_test("LastGraph", glines, GraphParsingError, exp_msg)
 
     glines[0] = "0\t10\t1\t1"
-    run_tempfile_test("LastGraph", glines, ValueError, exp_msg)
+    run_tempfile_test("LastGraph", glines, GraphParsingError, exp_msg)

metagenomescope/tests/assembly_graph_parser/test_parse_metacarvel_gml.py

@@ -1,5 +1,6 @@
 from networkx import NetworkXError
 from .utils import run_tempfile_test
+from metagenomescope.errors import GraphParsingError
 from metagenomescope.assembly_graph_parser import parse_metacarvel_gml
 
 
@@ -92,34 +93,34 @@ def test_parse_metacarvel_gml_insufficient_node_metadata():
     # Remove orientation from node 10
     mg.pop(5)
     exp_msg = 'Only 11 / 12 nodes have "orientation" given.'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
     # Remove length from node 10 (it's the line after the previous line we
     # removed)
     mg.pop(5)
     # due to "precedence" (just the order of iteration in the for loops), we
     # expect orientation to take priority over length in these error messages
     # -- but this doesn't really matter
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     # Restore mg
     mg = get_marygold_gml()
     # Now, just remove the length line. We should see an error message about
     # length, not orientation, now.
     mg.pop(6)
     exp_msg = 'Only 11 / 12 nodes have "length" given.'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
     # For fun, let's remove all of the lines with length and make sure this
     # updates the error msg accordingly
     mg = [line for line in mg if "length" not in line]
     exp_msg = 'Only 0 / 12 nodes have "length" given.'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     # ... And let's try that same thing with orientation, which as we've
     # established takes priority in error messages (again, doesn't actually
     # matter, but we might as well test that this behavior remains consistent)
     mg = [line for line in mg if "orientation" not in line]
     exp_msg = 'Only 0 / 12 nodes have "orientation" given.'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
 
 def test_parse_metacarvel_gml_insufficient_edge_metadata():
@@ -128,35 +129,35 @@ def test_parse_metacarvel_gml_insufficient_edge_metadata():
     # Remove orientation from edge 8 -> 9 (line 190 in the file)
     mg.pop(189)
     exp_msg = 'Only 15 / 16 edges have "orientation" given.'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
     # Remove orientation from all edges in the file
     mg = [
         line
         for line in mg
         if 'orientation "E' not in line and 'orientation "B' not in line
     ]
     exp_msg = 'Only 0 / 16 edges have "orientation" given.'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     # Restore mg
     mg = get_marygold_gml()
     # Remove mean from edge 12 -> 8
     mg.pop(182)
     exp_msg = 'Only 15 / 16 edges have "mean" given.'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
     # Also remove mean from edge 8 -> 9
     # This is actually line 191 of the file, but remember 0-indexing + already
     # popped one line above in the file
     mg.pop(189)
     exp_msg = 'Only 14 / 16 edges have "mean" given.'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     # Restore mg
     mg = get_marygold_gml()
     # Remove bsize from edge 7 -> 12
     mg.pop(168)
     exp_msg = 'Only 15 / 16 edges have "bsize" given.'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     # Remove stdev from edge 7 -> 9
     # Note that we haven't restored mg from above yet! This tests the whole
@@ -167,11 +168,11 @@ def test_parse_metacarvel_gml_insufficient_edge_metadata():
     # breaking this function.
     mg.pop(174)
     exp_msg = 'Only 15 / 16 edges have "stdev" given.'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     # Remove bsize from *all* lines -- stdev error should still show up
     mg = [line for line in mg if "bsize" not in line]
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
 
 def test_parse_metacarvel_gml_undirected_graph():
@@ -182,10 +183,10 @@ def test_parse_metacarvel_gml_undirected_graph():
     # Try two things: 1) the choice of directed/undirected isn't specified
     # (defaults to undirected), 2) explicitly specified as not directed
     mg.pop(1)
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     mg.insert(1, "  directed 0\n")
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
 
 def test_parse_metacarvel_gml_duplicate_edges():
@@ -221,7 +222,7 @@ def test_parse_metacarvel_gml_duplicate_edges():
     # detect that the input graph is a multigraph and be all like "nuh uh
     # you didn't get that from MetaCarvel, now did you" (something like that)
     run_tempfile_test(
-        "gml", mg, ValueError, "Multigraphs are unsupported", join_char=""
+        "gml", mg, GraphParsingError, "Multigraphs are unsupported", join_char=""
     )
 
 
@@ -294,7 +295,7 @@ def test_parse_metacarvel_gml_invalid_node_metadata():
         # angry if you put a string like FOW outside of quotes in a GML file.)
         p = "".join([c for c in o if c != '"'])
         exp_msg = 'Node NODE_10 has unsupported orientation "{}".'.format(p)
-        run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+        run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     # Test invalid lengths
     lengths = [
@@ -315,7 +316,7 @@ def test_parse_metacarvel_gml_invalid_node_metadata():
         exp_msg = 'Node NODE_10 has non-positive-integer length "{}".'.format(
             length_to_test
         )
-        run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+        run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
 
 def test_parse_metacarvel_gml_invalid_edge_metadata():
@@ -344,12 +345,12 @@ def test_parse_metacarvel_gml_invalid_edge_metadata():
         # (See test_parse_metacarvel_gml_invalid_node_metadata() above)
         p = "".join([c for c in val if c != '"'])
         exp_msg = 'has unsupported orientation "{}".'.format(p)
-        run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+        run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     mg.pop(189)
     mg.insert(189, '   orientation "REV"\n')
     exp_msg = 'has unsupported orientation "REV".'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     # Restoring the orientation to something normal (say, BB) should work
     mg.pop(189)
@@ -376,21 +377,21 @@ def test_parse_metacarvel_gml_invalid_edge_metadata():
         mg.insert(192, "   bsize {}\n".format(val))
         p = "".join([c for c in val if c != '"'])
         exp_msg = 'has non-positive-integer bsize "{}".'.format(p)
-        run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+        run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     # 3. Test mean
     mg = get_marygold_gml()
     mg.pop(198)
     mg.insert(198, '   mean "ABC"\n')
     exp_msg = 'has non-numeric mean "ABC".'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     # 4. Test stdev
     mg = get_marygold_gml()
     mg.pop(199)
     mg.insert(199, '   stdev "ABC"\n')
     exp_msg = 'has non-numeric stdev "ABC".'
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
     # TODO test bsize, mean, stdev more thoroughly
 
     # Test that NaN/infinity/zero/negative values work ok (but only with
@@ -461,14 +462,14 @@ def test_parse_metacarvel_gml_repeated_node_attrs():
     mg = get_marygold_gml()
     mg.insert(5, '   orientation "REV"\n')
     exp_msg = "Node NODE_10 has unsupported orientation \"['REV', 'FOW']\"."
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     mg = get_marygold_gml()
     mg.insert(5, '   length "200"\n')
     exp_msg = (
         "Node NODE_10 has non-positive-integer length \"['200', '100']\"."
     )
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
 
 def test_parse_metacarvel_gml_repeated_edge_attrs():
@@ -478,31 +479,31 @@ def test_parse_metacarvel_gml_repeated_edge_attrs():
         "Edge ('NODE_7', 'NODE_12') has unsupported orientation "
         "\"['EB', 'EB']\"."
     )
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     mg = get_marygold_gml()
     mg.insert(166, '   mean "123.45"\n')
     exp_msg = (
         "Edge ('NODE_7', 'NODE_12') has non-numeric mean "
         "\"['123.45', '-200.00']\"."
     )
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     mg = get_marygold_gml()
     mg.insert(166, '   stdev "123.45"\n')
     exp_msg = (
         "Edge ('NODE_7', 'NODE_12') has non-numeric stdev "
         "\"['123.45', 25.1234]\"."
     )
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
     mg = get_marygold_gml()
     mg.insert(167, "   bsize 15\n")
     exp_msg = (
         "Edge ('NODE_7', 'NODE_12') has non-positive-integer bsize "
         '"[15, 30]".'
     )
-    run_tempfile_test("gml", mg, ValueError, exp_msg, join_char="")
+    run_tempfile_test("gml", mg, GraphParsingError, exp_msg, join_char="")
 
 
 def test_parse_metacarvel_gml_repeated_edge_source_or_target():

metagenomescope/tests/assembly_graph_parser/test_validate_lastgraph.py

@@ -1,5 +1,6 @@
 import pytest
 from io import StringIO
+from metagenomescope.errors import GraphParsingError
 from metagenomescope.assembly_graph_parser import validate_lastgraph_file
 
 
@@ -9,9 +10,9 @@ def get_validate_err(glines):
     bad_lg = StringIO("\n".join(glines))
     # Assume that the LastGraph file represented by bad_lg will fail
     # validation, and return the accompanying error message.
-    # (If a ValueError *isn't* raised, this'll throw an error saying DID NOT
-    # RAISE or something.)
-    with pytest.raises(ValueError) as ei:
+    # (If a GraphParsingError *isn't* raised, this'll throw an error saying
+    # DID NOT RAISE or something.)
+    with pytest.raises(GraphParsingError) as ei:
         validate_lastgraph_file(bad_lg)
     return str(ei.value)