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

Question

大家好，我应该使用 Python 脚本从 vcf 文件中的 csv 文件中识别指定位置的可能 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

代码：

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)

Answer 1

如果例如 i = 'aa' 并且您执行 line = i.split(",") 这意味着 line = ['aa']，那么当您执行 line[2] + "_" + line[3] 时您将得到一个 IndexError 因为 line 没有第 2 个和第 3 个元素。

使用 try/except 或重新考虑代码的逻辑。

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

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

python

csv

error-handling

vcf-vcard

range