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get_final_emp_refsoil_abun.py
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get_final_emp_refsoil_abun.py
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#!/usr/bin/python
# usage: python get_final_emp_refsoil.py pytable.txt refsoil_filename.txt emp_final_refsoil.txt not_assigned.txt all.txt
# usage: python get_final_emp_refsoil_abun.py most_abun_filename.txt refsoil_filename.txt emp_final_refsoil_abun.txt not_assigned_abun.txt all_abun.txt
import sys
ftable = open(sys.argv[1],'r')
ffilename = open(sys.argv[2],'r')
fwrite = open(sys.argv[3],'w')
fwritenot = open(sys.argv[4],'w')
fwriteall = open(sys.argv[5],'w')
filetable = []
for line in ffilename:
sep = line.strip().split('\t')
filetable.append(sep)
#print filetable
for line in ftable:
idsep = line.strip().split('\t')
flag = 0
gi = []
for i in range(len(filetable)):
if (filetable[i][2]==idsep[2]):
fwrite.write(line.strip()+'\t'+filetable[i][0]+'\t'+filetable[i][1]+'\n')
gi.append(filetable[i][0])
flag = 1
if(flag == 0):
fwritenot.write(line.strip()+'\n')
fwriteall.write(line.strip()+'\n')
else:
fwriteall.write(line.strip()+'\t')
for i in gi:
fwriteall.write(i+'\t')
fwriteall.write('\n')