python 处理snp的vcf文件，统计snp在基因的intron、exon还是上游、下游还是不在基因及基因附近

1、c处理vcf文件，初步统计snp位置
位置信息有5种

down_stream是gene下游2k以内，up_stream 是gene上游2k以内，gene_exon是snp在外显子内，gene_intron是gene在内含子内，uninfluncial是gene不在上诉所有区域

SnpType.py
内容：

#这个脚本是用来看snp哪些是在基因中（分为exon和intron），哪些是在基因的上游、下游
#最终输出结果为：scaffold position 位置 geneid
#输入文件1：snpeff结果文件（/public/home/wangwen_lab/zhangjiexiong/Ageing/SNP/snpeff/snpeffC_F/02.runC/mor_imp_strictestfilter_Snp_AncRef_selected_anno4.vcf）
#输入文件2：gff3文件（/public/home/wangwen_lab/zhangjiexiong/Ageing/SNP/genome.gff3）

import sys,re
file1 = sys.argv[1]
file2 = sys.argv[2]
file3 = sys.argv[3]
f1 = open(file1,'r')
f2 = open(file2,'r')
f3 = open(file3,'w')
flag = 'fuck'
f1dick = {
   
   }
arr1 = []
for i in f1:
        if re.match("#",i):
                continue
        a = i.split("\t")
        if flag != a[0] and flag is not 'fuck':
                f1dick[flag] = arr1
                flag = a[0]
                arr1 = []
        #       print(a[0])
                arr1.append(a[1])
        elif flag is 'fuck':
                flag = a[0]
        else:
                arr1.append(a[1])
f1dick[flag] = arr1
#for i in f1dick:
#        print(i,f1dick[i])

sc = "fuck"
f2dick1 = {
   
   }
f2dick2 = {
   
   }
f2arr1 = []
for i in f2:
        if re.match("M",i) == None:
                f2dick1[geneid] = f2arr1
                continue
        a = i.split("\t")
        if a[2] == 'gene':
                f2arr1 = []
                f2arr1.append(a[3:5])
                if sc != a[0]:
                        f2dick2[sc] = f2dick1
                        f2dick1 = {
   
   }
                        sc = a[0]
                geneid = a[8].split(";")[0].split("=")[1]
        if a[2] == 'exon':
                f2arr1.append(a[3:5])
f2dick1[geneid] = f2arr1
f2dick2[sc] = f2dick1
del f2dick2['fuck']
f2.close()
for i in f1dick.keys():
        for j in f1dick[i]:#取到scaffold内的所有snp位点
                try:
                        taq = 0
                        for k in f2dick2