大家好,我应该使用Python脚本从vcf文件中的csv文件中的指定位置识别可能的SNP.
我刚开始使用python,可悲的是,我总是得到以下错误：

 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

码：

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)   

解决方法:

例如,如果i =’aa’并且执行line = i.split(“,”),则意味着line = [‘aa’],那么当您执行line [2]“ _” line [时,您将得到IndexError. 3],因为line没有第二和第三元素.

使用try / except或重新考虑代码的逻辑.