Fix previous commit (for EI-CoreBioinformatics#280)

Mikado/parsers/__init__.py

@@ -105,9 +105,15 @@ def __getstate__(self):
         state.update(self.__dict__)
         state["position"] = position
         if hasattr(self._handle, "filename"):
-            state["_handle"] = self._handle.filename
+            _handle = self._handle.filename
+            if isinstance(_handle, bytes):
+                _handle = _handle.decode()
+            state["_handle"] = _handle
         elif hasattr(self._handle, "name"):
-            state["_handle"] = self._handle.name
+            _handle = self._handle.name
+            if isinstance(_handle, bytes):
+                _handle = _handle.decode()
+            state["_handle"] = _handle
         else:
             raise TypeError("Unknown handle: {}".format(self._handle))
         return state

Mikado/scales/compare.py

@@ -608,7 +608,6 @@ def parse_prediction(args, index, queue_logger):
 
     queue_logger.info("Starting to parse the prediction")
     if args.processes > 1:
-        # print(mp.get_start_method())
         log_queue = args.log_queue
         dargs = dict()
         doself = False
@@ -624,7 +623,7 @@ def parse_prediction(args, index, queue_logger):
         assert os.path.exists(dump_dbhandle.name), dump_dbhandle.name
         assert os.stat(dump_dbhandle.name).st_size > 0, dump_dbhandle.name
         procs = [Assigners(index, nargs, queue, returnqueue, log_queue, counter, dump_dbhandle.name)
-                            for counter in range(1, args.processes)]
+                 for counter in range(1, args.processes)]
         [proc.start() for proc in procs]
         final_proc = FinalAssigner(index, nargs, returnqueue, log_queue=log_queue)
         final_proc.start()