def __init__(self, old_id_path, options, plus=False, log_info=None): # {
self.log_info = log_info
self.options = options
tool_name = "idmapper"
if plus: # {
tool_name = "idmapper_plus"
# } end if
self.command = [GetCommand(self, tool_name), "-s", "human", "-f", old_id_path]
DebugMsg(self, "Update command:\n %s" % (" ".join(self.command)))
self.stream = RunCommandFromList(self.command, stdout=STREAM_OUT, dpt=getattr(self.options, "dpt", False))
# ExtremeDebugMsg(self, " finished creating update stream")
self.GetLine()
class GeneIDUpdateStreamCls: # {
def __init__(self, old_id_path, options, plus=False, log_info=None): # {
self.log_info = log_info
self.options = options
tool_name = "idmapper"
if plus: # {
tool_name = "idmapper_plus"
# } end if
self.command = [GetCommand(self, tool_name), "-s", "human", "-f", old_id_path]
DebugMsg(self, "Update command:\n %s" % (" ".join(self.command)))
self.stream = RunCommandFromList(self.command, stdout=STREAM_OUT, dpt=getattr(self.options, "dpt", False))
# ExtremeDebugMsg(self, " finished creating update stream")
self.GetLine()
# ExtremeDebugMsg(self, " got the first line")
# } end def
def __iter__(self): # {
# ExtremeDebugMsg(self, "Creating iterator for GeneIDUpdateStreamCls")
return self
# } end def
# returns a dictionary: mapping[old_id] = set(new_ids)
def next(self): # {
# ExtremeDebugMsg(self, "In GeneIDUpdateStreamCls.next()...")
if getattr(self, "finished", False): # {
raise StopIteration
# } end if
if ID_UPDATE_HEADER != self.curr_line: # {
raise MainClassError('Invalid ID update header line: "%s"' % self.curr_line)
# } end if
mapping = dict()
self.GetLine()
# ExtremeDebugMsg(self, "Finished? %s" % getattr(self, "finished", False))
# ExtremeDebugMsg(self, "CURR LINE: %s" % self.curr_line)
while not getattr(self, "finished", False) and ID_UPDATE_HEADER != self.curr_line: # {
# ExtremeDebugMsg(self, " Processing update: %s" % self.curr_line)
(old_id, new_id) = self.curr_line.split(", ")[:2]
if "." in old_id: # {
old_id = old_id.split(".")[0]
# } end if
if "." in new_id: # {
new_id = new_id.split(".")[0]
# } end if
# ExtremeDebugMsg(self, " Old ID: %s, New ID: %s" % (old_id, new_id))
if old_id != new_id: # {
if old_id not in mapping: # {
mapping[old_id] = set()
# } end if
mapping[old_id].add(new_id)
# } end if
self.GetLine()
# } end while
return mapping
# } end def
def GetLine(self): # {
MAX_LOOPS = 100
count = 0
# self.GetRawLine()
next_line = ""
while not getattr(self, "finished", False) and "" == next_line: # {
# "" == getattr(self, "curr_line", "")): #{}
# self.GetRawLine()
next_line = self.stream.next()
# next() should return at least "\n" for a blank line
if "" == next_line: # {
# ExtremeDebugMsg(self, "STREAM COMPLETE")
self.finished = True
break
# } end if
next_line = CleanLine(next_line)
# ExtremeDebugMsg(self, "UPDATE LINE: %s" % next_line)
count += 1
if MAX_LOOPS < count: # {
raise MainClassError("Too many loops while getting update line!")
# } end if
# ExtremeDebugMsg(self, "POLLING STREAM")
# ret will be None until the process terminates
# ret = self.stream.poll()
# if (None != ret): #{
# ExtremeDebugMsg(self, "STREAM COMPLETE")
# self.finished = True
# } end if
# } end while
self.curr_line = next_line