gg2tax.py

#!/usr/bin/python
import sys


f = open(sys.argv[1],'r') #otu table in txt
ref = open(sys.argv[2],'r') #gg taxonomy file
g = open(sys.argv[3],'w') #output

data={}
for x in ref:

	data[x.split("\t")[0]]=x.split("\t")[1].rstrip("\n")
	

for i in f:
	
	if i[0]<>"#":
	
		k = i.split("\t")
		
		gg=k[0]
		
		try:
			tax=data[gg]
		except:
			tax="unknown"
			
		g.write(i.rstrip("\n")+"\t"+tax+"\n")
		
	else:
		g.write(i.rstrip("\n")+"\ttaxonomy\n")