大豆SNP位点查找V2.0
from time import perf_counter import csv import time start = perf_counter() f = open("GM18.txt" , "r") txt = f.read() #print(txt[:1000]) txt = txt.strip(">Gm18") txt = txt.replace("\n","").replace("\r","") #更改了此处的删除换行符！ # txt = txt.strip(r"\n") # txt = txt.strip(r"\r") txt = txt.strip("") #注意这个地方有错误就是开头的第一个字符串是1，光标位置是0。 #print(txt[:1000]) aimseq = input("请输入你想查找的DNA序列文件（回车结束）：") def indexstr(str1,str2): '''查找指定字符串str1包含指定子字符串str2的全部位置， 以列表形式返回''' lenth2=len(str2) lenth1=len(str1) indexstr2=[] i=0 while str2 in str1[i:]: indextmp = str1.index(str2, i, lenth1) indexstr2.append(indextmp) i = (indextmp + lenth2) return indexstr2 if __name__ == '__main__': print(indexstr(txt,aimseq)) pos = indexstr(txt,aimseq) # def getseq(): num = len(aimseq) for number in pos: if num == 45: sequence1 = txt[number - 300 : number] sequence2 = txt[number + 45 : number + 345] elif num == 50: sequence1 = txt[number - 300 : number] sequence2 = txt[number + 50 : number + 350] print("由以上条件我们可以得知前300个碱基为 {} ，后300个碱基为 {} ".format(sequence1,sequence2)) print("此次查找花费的时间是：{:.5f} 秒".format(perf_counter() - start)) c= open ("SNP相关数据.csv","w+") writer=csv.writer(c) datalist = [] datalist.append(aimseq) time.sleep(0.1) datalist.append(sequence1) time.sleep(0.1) datalist.append(sequence2) time.sleep(0.1) for numbers in pos: datalist.append(numbers) time.sleep(0.1) writer.writerow(["SNP","前300个碱基","后300个碱基","所在位置"]) writer.writerow(datalist) c.close()