def test_basic_file_op():
filename = "test_data/test_python"
fd = open(filename, "wb")
bd = jeweler_pb2.BraceletData()
bd.name = "TEST"
zleveldb.write_protobuf_data(fd, bd)
fd.close()
fd = open(filename, "rb")
bd = jeweler_pb2.BraceletData()
zleveldb.load_protobuf_data(fd, bd)
assert("TEST" == bd.name)
def generate_training_data(self):
ret = []
data = jeweler_pb2.BraceletData()
fd = open(self.shop_info.bracelet_file, "rb")
while zleveldb.load_protobuf_data(fd, data):
for gene in data.related_transcript:
ret.append(GeneRelationship(data, gene, self))
return ret
def load_bracelet_data(self):
graphs = list()
graph_index = dict()
data = jeweler_pb2.BraceletData()
fd = open(self.shop_info.bracelet_file, "rb")
while zleveldb.load_protobuf_data(fd, data):
if data.num_read == 0:
self.black_list.add(data.name)
if len(data.related_transcript) == 0:
continue
graph = graph_index.get(data.name, None)
if not graph:
graph = nx.Graph()
graphs.append(graph)
graph_index[data.name] = graph
for gene in data.related_transcript:
graph_index[gene.name] = graph
graph.add_edge(data.name, gene.name, label=gene.num_shared_read)
self.add_node_color(graph, gene.name)
self.add_node_color(graph, data.name)
self.register_edge(data.name, gene.name)
return graphs
