Python IndexError: list index out of range while finding SNPs in vcf

Question

Hi all I am supposed to use a Python script to identify possible SNPs at specified positions from a csv file in vcf files.
I just started using python and sadly I always get following Error :

 Traceback (most recent call last):
 File "getSNPs.py", line 20, in <module>    oo = line[2] + "_" +
 line[3]
 IndexError: list index out of range from the following script
 !/bin/python usage: python getSNPs.py your.vcf PhenoSNPs.csv

Code:

import sys
import gzip

SNPs = {}

for i in gzip.open(sys.argv[1], "r"):
    if '#' not in i:
        line = i.split("\t")
        oo = line[0] + "_" + line[1]
        SNPs[oo] = i

pp = sys.argv[1] + ".captureSNPs"

out = open(pp, "w")

for i in open(sys.argv[2], "r"):
    line = i.split(",")
    oo = line[2] + "_" + line[3]
    try:
        out.write(SNPs[oo])
    except KeyError:
        ow = line[2] + "\t" + line[3] + "\t" + "not covered" + "\n"
        out.write(ow)   

Answer 1

If for instance i = 'aa' and you do line = i.split(",") it implies that line = ['aa'], then you will get an IndexError when you do line[2] + "_" + line[3] because line doesn't have 2nd and 3rd elements.

Use try/except or re-think the logic of your code.