#!/usr/bin/python
# Rewrites SNVMix2 output into tab separated format to be inserted into psql
import sys,os
header='gene\tposition\tref\tsnv\treads\taa\tab\tbb\tmaxp\n'
fn=sys.argv[1]
ofn='%st.txt' % os.path.splitext(fn)[0]
open(ofn,'w').write(header)
for i in open(fn):
 isp=i.strip().split('\t')
 outlist=isp[0].split(':')
 outlist.append(isp[1])
 outlist.append(isp[2])
 outlist.append(','.join(isp[3].split(',')[:2]))
 outlist+=isp[3].split(',')[2:]
 open(ofn,'a').write('\t'.join(outlist)+'\n')