生信编程实战第10题（python）

题目来自生信技能树论坛

image.png

先下载tss文件

wget http://www.biotrainee.com/jmzeng/tmp/hg38.tss

chr7        148697841        148698941
chr7        148698942        148699029
chr7        148699911        148701053
chr7        148701109        148701307
chr7        148701354        148702694
chr7        148703100        148703520
chr7        148703831        148704175
chr7        148704484        148704734
chr7        148704857        148705937
chr7        148706271        148706671

然后针对这些位点操作

脚本如下：

import sys
args=sys.argv
filename1=args[1]
filename2=args[2]
aDict={}

for line in open (filename1):
   lineL=line.strip().split("\t")
   gene_ID=lineL[0]
   chr_name=lineL[1]
   start=lineL[2]
   end=lineL[3]
   if chr_name not in aDict:
     aDict[chr_name]={}
   aDict[chr_name][start,end]=gene_ID


for line in open (filename2):
   lineList=line.strip().split("\t")
   Chr_name=lineList[0]
   Start=int(lineList[1])
   End=int(lineList[2])
   for k1,v1 in aDict[Chr_name].items():
     if int(k1[0])<=Start <= int(k1[1]) or int(k1[0])<=End <= int(k1[1]) or Start <=int(k1[0])<=End or Start <=int(k1[1])<=End :
        print(Chr_name,Start,End,v1)

根据不同的情景，对倒数第二行的if条件进行改变即可

python3 exercise.py hg38.tss test.txt

chr7 148697841 148698941 NM_003592
chr7 148698942 148699029 NM_003592
chr7 148699911 148701053 NM_003592

10个中只找到这3个