def DummyNeighbors(allProts, path, stpFile, dnFile, neighborType):
prizes = set()
with open(os.path.join(path, stpFile)) as f:
for line in f:
parts = line.split()
# mRNAs can't be Steiner nodes
if parts[0] == "W" and not parts[1].endswith("_MRNA"):
prizes.add(parts[1])
psNodes = allProts.difference(prizes)
if neighborType == "prizes":
NetworkUtil.WriteCollection(os.path.join(path, dnFile), prizes)
elif neighborType == "nonprizes":
NetworkUtil.WriteCollection(os.path.join(path, dnFile), psNodes)
else:
raise RuntimeError(
"%s is not a valid type of dummy node neighbor connection" %
neighborType)
return psNodes
