finalFilter.py

#!/bin/env python
'''
finalFilter.py

Copyright (c) 2015, David Edwards, Bernie Pope, Kat Holt
All rights reserved. (see README.txt for more details)


example: 
python finalFilter.py <raw>.vfc <q30>.vcf <outHetFile> <HetsVCF>

Created:	24/01/2013
Modified:	02/09/2015
author: David Edwards
'''
import sys
from pipe_utils import (splitPath)

inFile = sys.argv[1]
outFile = sys.argv[2]
(prefix,middle,ext) = splitPath(outFile)

outHetFile = sys.argv[3] + '/' + middle[:-3] + "het.txt"
if sys.argv[4] == "True":
    HetsVCF = True
else:
    HetsVCF = False
vcfIn = open(inFile)
vcfOut = open(outFile, "w")
hetOut = open(outHetFile, "w")
if HetsVCF:
    outHetPosFile = prefix + '/' + middle[:-3] + "het.vcf"
    hetVcfOut = open(outHetPosFile,"w")
hetCount = 0

for line in vcfIn:
    if line.startswith("#") == True:
        vcfOut.write(line)
        if HetsVCF:
        	hetVcfOut.write(line)
    else:
        element = line.split("\t")
        if element[5] >= 30:       
            if len(element[4].split(",")) <= 2:
                vcfOut.write(line)    
            elif element[7].startswith("IND") != True:
                hetCount += 1
                if HetsVCF:
                    hetVcfOut.write(line)

hetOut.write(str(hetCount))
hetOut.close()
vcfOut.close()
vcfIn.close()
if HetsVCF:
	hetVcfOut.close()