#!/usr/bin/python
# this script find full taxonomy from file of tax ID
# usage: python id_to_tax.py id_file.txt > full_tax.txt
import sys
import taxonomy_finder
for line in open(sys.argv[1], "r"):
print line.strip() + "\t" + taxonomy_finder.from_id(line.strip())
#print len(dict)
#process normal_counts
count = open(sys.argv[1],'r')
fwrite = open(sys.argv[4],'w')
lines = count.next()
fwrite.write(lines.strip()+'\t'+'organism'+'\t'+'function'+'\t'+'ec'+'\t'+'full_tax'+'\n')
for line in count:
splt = line.strip().split('\t')
organism = "null"
function = "null"
ecnum = "null"
fulltax = "null"
if(dict.has_key(splt[0])):
md5 = dict[splt[0]][0]
function = dict[splt[0]][2]
ecs = function.split("EC:")
if(len(ecs)>1):
ec = ecs[1].split(")")
ecnum = ec[0]
if(ordict.has_key(splt[0])):
organism = ordict[splt[0]][2]
taxid = mg_rast_jason.get_taxid(md5)
if(str(taxid)!="null"):
fulltax = taxonomy_finder.from_id(str(taxid))
fwrite.write(line.strip()+'\t'+ organism+'\t' + function+'\t'+ecnum+'\t'+fulltax+'\n')
#!/usr/bin/python
#this script find full taxonomy from file of tax ID
#usage: python id_to_tax.py id_file.txt > full_tax.txt
import sys
import taxonomy_finder
for line in open(sys.argv[1], 'r'):
print line.strip() + "\t" + taxonomy_finder.from_id(line.strip())
