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_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_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
