new_contents: import sys
  import os
  
  #def count_id(ids):
  tip = sys.argv[1]
  n = 1
  IDs={}
  for line in open(tip, 'rU'):
  	line = line.strip().split("|")
  	oid = line[0]
  	if oid not in IDs:
  		IDs[oid] = [n, tip.split(".")[0]]
  	else:
  		IDs[oid] = [n+1, tip.split(".")[0]]
  
  for keys in IDs:
  	print "%s\t%s\t%s" %(keys, IDs[keys][0], IDs[keys][1])
  
subject: split oid|geneid, dereplicate by oid, count the number of times oid appeared in the file, write out file (tip node) name as well