def test_iter_over_colors_json_ids(self):
# when multiedge is serialized into json a list of colors in it referenced by their ids
# the multiplicity of colors has to be preserved
v1 = BlockVertex("v1")
v2 = BlockVertex("v2")
genomes = [
self.genome1, self.genome1, self.genome2, self.genome3,
self.genome2
]
multicolor = Multicolor(*genomes)
bgedge = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
json_ids = bgedge.colors_json_ids
self.assertTrue(isinstance(json_ids, list))
json_ids_list = json_ids
self.assertEqual(len(json_ids_list), 5)
ref_json_ids = Counter(genome.json_id for genome in genomes)
res_json_ids = Counter(json_ids_list)
self.assertDictEqual(ref_json_ids, res_json_ids)
# case when color objects are not a BGGenome, but some other hashable object without json_id attribute
v1 = BlockVertex("v1")
v2 = BlockVertex("v2")
colors = ["red", "red", "green", "black", "yellow", "green"]
multicolor = Multicolor(*colors)
bgedge = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
json_ids = bgedge.colors_json_ids
self.assertTrue(isinstance(json_ids, list))
json_ids_list = json_ids
self.assertEqual(len(json_ids_list), 6)
ref_json_ids = Counter(hash(genome) for genome in colors)
res_json_ids = Counter(json_ids_list)
self.assertDictEqual(ref_json_ids, res_json_ids)
# case when color objects are mixed objects: BGGenome objects, just hashable, have json_id but not BGGenome
v1 = BlockVertex("v1")
v2 = BlockVertex("v2")
mock1, mock2 = Mock(), Mock()
mock1.json_id = 5
mock2.json_id = 6
colors = [
self.genome1, mock1, self.genome2, "black", mock2, self.genome2
]
multicolor = Multicolor(*colors)
bgedge = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
json_ids = bgedge.colors_json_ids
self.assertTrue(isinstance(json_ids, list))
json_ids_list = list(json_ids)
self.assertEqual(len(json_ids_list), 6)
ref_json_ids = Counter(
genome.json_id if hasattr(genome, "json_id") else hash(genome)
for genome in colors)
res_json_ids = Counter(json_ids_list)
self.assertDictEqual(ref_json_ids, res_json_ids)
def test_data_update_non_dict_source(self):
edge = BGEdge(
vertex1=TaggedBlockVertex("v1"),
vertex2=TaggedBlockVertex("v2"),
multicolor=Multicolor(self.genome1, self.genome2),
data={"fragment": {
"name": "scaffold2",
"origin": "test"
}})
for source in [1, "2", Multicolor(), (1, ), [
2,
]]:
with self.assertRaises(ValueError):
edge.update_data(source=source)
def test_is_irregular_edge(self):
# and edge is called an irregular edge if at least one of its vertices is an irregular vertex
v1 = BlockVertex("v1")
v2 = BlockVertex("v2")
v3 = InfinityVertex("v3")
multicolor = Multicolor(self.genome3)
edge1 = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
edge2 = BGEdge(vertex1=v1, vertex2=v3, multicolor=multicolor)
edge3 = BGEdge(vertex1=v3, vertex2=v1, multicolor=multicolor)
edge4 = BGEdge(vertex1=v3, vertex2=v3, multicolor=multicolor)
self.assertFalse(edge1.is_irregular_edge)
self.assertTrue(edge2.is_irregular_edge)
self.assertTrue(edge3.is_irregular_edge)
self.assertTrue(edge4.is_irregular_edge)
def test_merging_correct(self):
# two BGEdges can be merged together into a third, separate BGEdge
# that would contain information from both supplied BGEdges in terms of colors and multiplicities
# such merge is allowed only if a pair of vertices in both BGEdges is the same
# ordering of vertices if not a concern, since edges in BreakpointGraph are not directed
v1 = BlockVertex("v1")
v2 = BlockVertex("v2")
multicolor = Multicolor(self.genome3)
multicolor1 = Multicolor(self.genome2)
edge1 = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
edge2 = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor1)
merged_edge = BGEdge.merge(edge1, edge2)
self.assertEqual(merged_edge.vertex1, v1)
self.assertEqual(merged_edge.vertex2, v2)
self.assertEqual(merged_edge.multicolor, multicolor + multicolor1)
def test_initialization_non_empty_data_attribute(self):
v1 = TaggedBlockVertex("v1")
v2 = TaggedBlockVertex("v2")
multicolor = Multicolor(self.genome1)
data = {"fragment": {"name": "scaffold1"}}
edge = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor, data=data)
self.assertDictEqual(edge.data, data)
def test_initialization(self):
# simple correct initialization of BGEdge instance
v1 = BlockVertex("v1")
v2 = BlockVertex("v2")
multicolor = Multicolor(self.genome3)
edge = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
self.assertEqual(edge.vertex1, v1)
self.assertEqual(edge.vertex2, v2)
self.assertEqual(edge.multicolor, multicolor)
def test_data_update_empty_source(self):
edge = BGEdge(
vertex1=TaggedBlockVertex("v1"),
vertex2=TaggedBlockVertex("v2"),
multicolor=Multicolor(self.genome1, self.genome2),
data={"fragment": {
"name": "scaffold2",
"origin": "test"
}})
update_source = {}
edge.update_data(source=update_source)
self.assertTrue(
dicts_are_equal(
edge.data,
{"fragment": {
"name": "scaffold2",
"origin": "test"
}}))
def test_data_update(self):
update_source = {"fragment": {"name": "scaffold11"}}
edge = BGEdge(
vertex1=TaggedBlockVertex("v1"),
vertex2=TaggedBlockVertex("v2"),
multicolor=Multicolor(self.genome1, self.genome2),
data={"fragment": {
"name": "scaffold2",
"origin": "test"
}})
edge.update_data(source=update_source)
self.assertIsInstance(edge.data, dict)
self.assertIn("fragment", edge.data)
self.assertIsInstance(edge.data["fragment"], dict)
self.assertIn("name", edge.data["fragment"])
self.assertIn("origin", edge.data["fragment"])
self.assertEqual(edge.data["fragment"]["name"], "scaffold11")
self.assertEqual(edge.data["fragment"]["origin"], "test")
def get_full_support_edge(regular_vertex1, regular_vertex2, data):
bg = data["gos-asm"]["bg"]
multicolor = Multicolor(*[
color
for bgedge in bg.edges_between_two_vertices(vertex1=regular_vertex1,
vertex2=regular_vertex2)
for color in bgedge.multicolor.colors
])
return BGEdge(vertex1=regular_vertex1,
vertex2=regular_vertex2,
multicolor=multicolor)
def test_json_deserialization_supplied_schema(self):
# when a scheme is supplied it shall be used for deserialization
# correct case no information in json object about schema
class BGEdgeJSONSchemeDefaultVertex1(BGEdge.BGEdgeJSONSchema):
vertex1_id = fields.Int(attribute="vertex1_json_id",
required=False,
default=1,
missing=1)
json_object = {
"vertex1_id": 1,
"vertex2_id": 2,
"multicolor": [1, 2, 3, 4]
}
result = BGEdge.from_json(
data=json_object, json_schema_class=BGEdgeJSONSchemeDefaultVertex1)
self.assertTrue(isinstance(result, BGEdge))
self.assertEqual(result.vertex1, 1)
self.assertEqual(result.vertex2, 2)
self.assertListEqual(result.multicolor, [1, 2, 3, 4])
# correct case with information about json object schema
# such information about json schema shall be ignored at the BGEdge deserialization level
json_object = {
BGEdge_JSON_SCHEMA_JSON_KEY: "dummy_string",
"vertex1_id": 1,
"vertex2_id": 2,
"multicolor": [1, 2, 3, 4]
}
result = BGEdge.from_json(
data=json_object, json_schema_class=BGEdgeJSONSchemeDefaultVertex1)
self.assertTrue(isinstance(result, BGEdge))
self.assertEqual(result.vertex1, 1)
self.assertEqual(result.vertex2, 2)
self.assertListEqual(result.multicolor, [1, 2, 3, 4])
# incorrect case with at least one vertex id not present in json object
json_object = {"vertex2_id": 2, "multicolor": [1, 2, 3, 4]}
result = BGEdge.from_json(
data=json_object, json_schema_class=BGEdgeJSONSchemeDefaultVertex1)
self.assertTrue(isinstance(result, BGEdge))
self.assertEqual(result.vertex1, 1)
self.assertEqual(result.vertex2, 2)
self.assertListEqual(result.multicolor, [1, 2, 3, 4])
json_object = {"vertex1_id": 2, "multicolor": [1, 2, 3, 4]}
with self.assertRaises(ValidationError):
BGEdge.from_json(data=json_object)
# incorrect case with no multicolor present in json object
json_object = {
"vertex2_id": 2,
"vertex1_id": 1,
}
with self.assertRaises(ValidationError):
BGEdge.from_json(data=json_object)
def test_json_deserialization_default_schema(self):
# with no scheme is supplied, default scheme for the BGVertex is applied
# deserialization for vertices and multicolor shall be performed as is, but then it will be resupplied from
# the overviewing BreakpointGraph
# correct case no information in json object about schema
json_object = {
"vertex1_id": 1,
"vertex2_id": 2,
"multicolor": [1, 2, 3, 4]
}
result = BGEdge.from_json(data=json_object)
self.assertTrue(isinstance(result, BGEdge))
self.assertEqual(result.vertex1, 1)
self.assertEqual(result.vertex2, 2)
self.assertListEqual(result.multicolor, [1, 2, 3, 4])
# correct case with information about json object schema
# such information about json schema shall be ignored at the BGEdge deserialization level
json_object = {
BGEdge_JSON_SCHEMA_JSON_KEY: "dummy_string",
"vertex1_id": 1,
"vertex2_id": 2,
"multicolor": [1, 2, 3, 4]
}
result = BGEdge.from_json(data=json_object)
self.assertTrue(isinstance(result, BGEdge))
self.assertEqual(result.vertex1, 1)
self.assertEqual(result.vertex2, 2)
self.assertListEqual(result.multicolor, [1, 2, 3, 4])
# incorrect case with at least one vertex id not present in json object
json_object = {"vertex2_id": 2, "multicolor": [1, 2, 3, 4]}
with self.assertRaises(ValidationError):
BGEdge.from_json(data=json_object)
json_object = {"vertex1_id": 2, "multicolor": [1, 2, 3, 4]}
with self.assertRaises(ValidationError):
BGEdge.from_json(data=json_object)
# incorrect case with no multicolor present in json object
json_object = {
"vertex2_id": 2,
"vertex1_id": 1,
}
with self.assertRaises(ValidationError):
BGEdge.from_json(data=json_object)
def get_breakpoint_graph(stream, merge_edges=True):
""" Taking a file-like object transforms supplied gene order data into the language of
:param merge_edges: a flag that indicates if parallel edges in produced breakpoint graph shall be merged or not
:type merge_edges: ``bool``
:param stream: any iterable object where each iteration produces a ``str`` object
:type stream: ``iterable`` ver ``str``
:return: an instance of a BreakpointGraph that contains information about adjacencies in genome specified in GRIMM formatted input
:rtype: :class:`bg.breakpoint_graph.BreakpointGraph`
"""
result = BreakpointGraph()
current_genome = None
fragment_data = {}
for line in stream:
line = line.strip()
if len(line) == 0:
###############################################################################################
#
# empty lines are omitted
#
###############################################################################################
continue
if GRIMMReader.is_genome_declaration_string(data_string=line):
###############################################################################################
#
# is we have a genome declaration, we must update current genome
# all following gene order data (before EOF or next genome declaration) will be attributed to current genome
#
###############################################################################################
current_genome = GRIMMReader.parse_genome_declaration_string(
data_string=line)
fragment_data = {}
elif GRIMMReader.is_comment_string(data_string=line):
if GRIMMReader.is_comment_data_string(string=line):
path, (key, value) = GRIMMReader.parse_comment_data_string(
comment_data_string=line)
if len(path) > 0 and path[0] == "fragment":
add_to_dict_with_path(destination_dict=fragment_data,
key=key,
value=value,
path=path)
else:
continue
elif current_genome is not None:
###############################################################################################
#
# gene order information that is specified before the first genome is specified can not be attributed to anything
# and thus omitted
#
###############################################################################################
parsed_data = GRIMMReader.parse_data_string(data_string=line)
edges = GRIMMReader.get_edges_from_parsed_data(
parsed_data=parsed_data)
for v1, v2 in edges:
edge_specific_data = {
"fragment": {
"forward_orientation": (v1, v2)
}
}
edge = BGEdge(vertex1=v1,
vertex2=v2,
multicolor=Multicolor(current_genome),
data=deepcopy(fragment_data))
edge.update_data(source=edge_specific_data)
result.add_bgedge(bgedge=edge, merge=merge_edges)
return result
def test_is_bgedge_vtree_consistent(self):
v1, v2 = "v1", "v2"
bgedge = BGEdge(vertex1=v1, vertex2=v2, multicolor=Multicolor())
##########################################################################################
#
# bgedge with an empty multicolor complies with any tree
#
##########################################################################################
mc = Multicolor()
bgedge.multicolor = mc
self.assertTrue(BGTree("(v1, v2);").bgedge_is_vtree_consistent(bgedge))
##########################################################################################
#
# simple cases
#
##########################################################################################
tree = BGTree("(((v1, v2), v3),(v4, v5));")
bgedge.multicolor = Multicolor(self.bg_v1)
self.assertTrue(tree.bgedge_is_vtree_consistent(bgedge))
##########################################################################################
#
# a small v1, v2 subtree, still consistent
#
##########################################################################################
bgedge.multicolor = Multicolor(self.bg_v1, self.bg_v2)
self.assertTrue(tree.bgedge_is_vtree_consistent(bgedge))
##########################################################################################
#
# bigger v1, v2, v3 subtree, still consistent
#
##########################################################################################
bgedge.multicolor = Multicolor(self.bg_v1, self.bg_v2, self.bg_v3)
self.assertTrue(tree.bgedge_is_vtree_consistent(bgedge))
##########################################################################################
#
# v2, v3 is not a valid subtree (its compliment is two subtrees, instead of one)
#
##########################################################################################
bgedge.multicolor = Multicolor(self.bg_v2, self.bg_v3)
self.assertFalse(tree.bgedge_is_vtree_consistent(bgedge))
##########################################################################################
#
# if some genomes in multicolor are not present in tree, then multicolor will not be consistent with the tree
#
##########################################################################################
bgedge.multicolor = Multicolor(self.bg_v1, BGGenome("v6"))
self.assertFalse(tree.bgedge_is_vtree_consistent(bgedge))
##########################################################################################
#
# other cases for a non wgd tree
#
##########################################################################################
bgedge.multicolor = Multicolor(self.bg_v1, self.bg_v2, self.bg_v3,
self.bg_v4)
self.assertFalse(tree.bgedge_is_vtree_consistent(bgedge))
bgedge.multicolor = Multicolor(self.bg_v1, self.bg_v2, self.bg_v3,
self.bg_v5)
self.assertFalse(tree.bgedge_is_vtree_consistent(bgedge))
bgedge.multicolor = Multicolor(self.bg_v1, self.bg_v2, self.bg_v4,
self.bg_v5)
self.assertFalse(tree.bgedge_is_vtree_consistent(bgedge))
bgedge.multicolor = Multicolor(self.bg_v1, self.bg_v3, self.bg_v4,
self.bg_v5)
self.assertFalse(tree.bgedge_is_vtree_consistent(bgedge))
bgedge.multicolor = Multicolor(self.bg_v2, self.bg_v3, self.bg_v4,
self.bg_v5)
self.assertFalse(tree.bgedge_is_vtree_consistent(bgedge))
bgedge.multicolor = Multicolor(self.bg_v1, self.bg_v2, self.bg_v3,
self.bg_v4, self.bg_v5)
self.assertTrue(tree.bgedge_is_vtree_consistent(bgedge))
bgedge.multicolor = Multicolor(self.bg_v5, self.bg_v4)
self.assertTrue(tree.bgedge_is_vtree_consistent(bgedge))
bgedge.multicolor = Multicolor(self.bg_v3, self.bg_v4, self.bg_v5)
self.assertFalse(tree.bgedge_is_vtree_consistent(bgedge))
bgedge.multicolor = Multicolor(self.bg_v3, self.bg_v5)
self.assertFalse(tree.bgedge_is_vtree_consistent(bgedge))
def test_equality(self):
# edges are called equal if they connect same pairs of vertices and have same multicolor assigned to them
v1 = BlockVertex("v1")
v2 = BlockVertex("v2")
v3 = BlockVertex("v3")
v4 = BlockVertex("v4")
multicolor = Multicolor(self.genome3)
multicolor1 = Multicolor(self.genome2)
edge1 = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
edge2 = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor1)
edge3 = BGEdge(vertex1=v1, vertex2=v3, multicolor=multicolor1)
edge4 = BGEdge(vertex1=v3, vertex2=v4, multicolor=multicolor)
self.assertNotEqual(edge1, edge2)
self.assertNotEqual(edge1, edge3)
self.assertNotEqual(edge2, edge3)
self.assertNotEqual(edge1, edge4)
edge4 = BGEdge(vertex1=v2, vertex2=v1, multicolor=multicolor)
edge5 = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
self.assertEqual(edge1, edge4)
self.assertEqual(edge1, edge5)
self.assertEqual(edge4, edge5)
self.assertNotEqual(edge1, 5)
edge6 = BGEdge(vertex1=v3, vertex2=v1, multicolor=multicolor)
self.assertNotEqual(edge1, edge6)
self.assertEqual(edge1, edge4)
edge4.data = {"fragment": {"name": 1}}
edge1.data = {"fragment": {"name": 2}}
self.assertNotEqual(edge1, edge4)
edge1.data = {"fragment": {"name": 1}}
self.assertEqual(edge1, edge4)
def test_merging_incorrect(self):
# cases when vertices in two supplied for the merging edges are not consistent
v1 = BlockVertex("v1")
v2 = BlockVertex("v2")
v3 = BlockVertex("v3")
v4 = BlockVertex("v4")
multicolor = Multicolor(self.genome3)
multicolor1 = Multicolor(self.genome2)
edge1 = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
edge2 = BGEdge(vertex1=v1, vertex2=v3, multicolor=multicolor1)
with self.assertRaises(ValueError):
BGEdge.merge(edge1, edge2)
edge2 = BGEdge(vertex1=v3, vertex2=v2, multicolor=multicolor1)
with self.assertRaises(ValueError):
BGEdge.merge(edge1, edge2)
edge2 = BGEdge(vertex1=v3, vertex2=v4, multicolor=multicolor1)
with self.assertRaises(ValueError):
BGEdge.merge(edge1, edge2)
edge2 = BGEdge(vertex1=v1, vertex2=v1, multicolor=multicolor1)
with self.assertRaises(ValueError):
BGEdge.merge(edge1, edge2)
edge2 = BGEdge(vertex1=v2, vertex2=v2, multicolor=multicolor1)
with self.assertRaises(ValueError):
BGEdge.merge(edge1, edge2)
edge2 = BGEdge(vertex1=v3, vertex2=v1, multicolor=multicolor1)
with self.assertRaises(ValueError):
BGEdge.merge(edge1, edge2)
def test_json_serialization(self):
# simple case of serialization, single color, no multiplicity
v1, v2 = BlockVertex("v1"), BlockVertex("v2")
color1 = BGGenome("genome1")
multicolor = Multicolor(color1)
edge = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
ref_result = {
"vertex1_id": v1.json_id,
"vertex2_id": v2.json_id,
"multicolor": [color1.json_id]
}
self.assertDictEqual(edge.to_json(schema_info=False), ref_result)
# case where multiple colors are present, multiplicity is 1 for every of them
color2 = BGGenome("genome2")
multicolor = Multicolor(color1, color2)
edge = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
result = edge.to_json()
self.assertTrue(isinstance(result, dict))
self.assertEqual(result["vertex1_id"], v1.json_id)
self.assertEqual(result["vertex2_id"], v2.json_id)
self.assertSetEqual(set(result["multicolor"]),
{color1.json_id, color2.json_id})
self.assertEqual(result[BGEdge_JSON_SCHEMA_JSON_KEY],
edge.json_schema_name)
# case where multiple colors are present, multiplicity is both 1 and greater than 1
color3 = BGGenome("genome3")
multicolor = Multicolor(color1, color1, color1, color2, color2, color3)
edge = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
result = edge.to_json(schema_info=False)
self.assertTrue(isinstance(result, dict))
self.assertEqual(result["vertex1_id"], v1.json_id)
self.assertEqual(result["vertex2_id"], v2.json_id)
self.assertSetEqual(set(result["multicolor"]),
{color1.json_id, color2.json_id, color3.json_id})
self.assertDictEqual(
Counter(result["multicolor"]),
Counter(color.json_id
for color in multicolor.multicolors.elements()))
# weird case when a vertex1/vertex attribute in edge is not an instance of BGVertex
# and moreover it does not have "json_id" attribute
edge = BGEdge(vertex1=v1, vertex2=1, multicolor=Multicolor(color1))
result = edge.to_json()
self.assertTrue(isinstance(result, dict))
self.assertEqual(result["vertex1_id"], v1.json_id)
self.assertEqual(result["vertex2_id"], hash(1))
self.assertListEqual(result["multicolor"], [color1.json_id])
self.assertEqual(result[BGEdge_JSON_SCHEMA_JSON_KEY],
edge.json_schema_name)
def test_empty_initialization_incorrect(self):
with self.assertRaises(TypeError):
# a BGEdge wrapper is meant to wrap something, but not nothing
BGEdge()
def test_initialization_empty_data_attribute(self):
v1 = TaggedBlockVertex("v1")
v2 = TaggedBlockVertex("v2")
multicolor = Multicolor(self.genome1)
edge = BGEdge(vertex1=v1, vertex2=v2, multicolor=multicolor)
self.assertDictEqual(edge.data, BGEdge.create_default_data_dict())