Question

感谢您的帮助和抱歉我的天真我需要生成一些单词的排列（ATGC）实际上是用于二组分的核苷酸（例如AA AT AG AC），三组分（AAA AAT AAC AAG），四，五等（一次一个），然后检查包含具有某些值的序列的其他文件，每个排列的出现次数。我生成了排列列表。现在我只需循环遍历序列（从值中拆分序列）来计算上面生成的每个排列，并在新文件中获得输出。但我只得到一个序列的答案，而不是其他序列的答案。

我试图遵循的程序逻辑是：

在file1中生成ATCG的排列（例如AT AG AC AA ......）
读取生成的file1和序列#value文件（DNA_seq_val.txt）
阅读序列并将序列分开形式值
遍历排列的序列并打印它们在结果文件中出现值（每个用逗号分隔）。

输入测试文件= DNA_seq_val.txt AAAATTTT＃99 \ n CCCCGGGG＃77 \ n ATATATCGCGCG＃88 \ n

*我得到的输出是 - 2,0,0,1,0,0,0,0,0,0,0,0,0,0,2,99 AAAATTTT \ n 77 CCCCGGGG \ n 88 ATATATCGCGCG 需要的输出是 2,0,0,1,0,0,0,0,0,0,0,0,0,0,2,99 AAAATTTT \ n x，x，x，x，x，x，x，x，x，x，x，x，x，x，x，x，77 CCCCGGGGx \ n x，x，x，x，x，x，x，x，x，x，x，x，x，x，x，x，88 ATATATCGCGCG（其中x =第一行中的对应计数）

    enter code herefrom itertools import product
import os

f2 = open('TRYYY', 'a')

#********Generate the permutations start********
per = product('ACGT', repeat=2) # ATGC =nucleotides; 2= for di ntd(replace 2 with 3 fir tri ntds and so on)
f = open('myfile', 'w')
p = ""
for p in per:
    p = "".join(p)
    f.write(p + "\n")
f.close()

#********Generate the permutations ENDS********

with open('DNA_seq_val.txt', 'r+') as SEQ, open('myfile', 'r+') as TET: #open two files
    SEQ_lines = sum(1 for line in open('DNA_seq_val.txt'))      #count lines in sequences file
    #print (SEQ_lines)
    compo_lines = sum(1 for line in open('myfile'))     #count lines in composition
    #print (compo_lines)
    for lines in SEQ:
        line,val1 = lines.split("#")
        val2 = val1.rstrip('\n')
        val = str(val2)
        line = line.rstrip('\n')
        length =len(line)
        #print (line)       
        #print (val)
        LIN = line, val
        #print (LIN)
        newstr = "".join((line))
        print (newstr)
        #while True:        # infinte loop
        for PER in TET:
            #print (line)
            PER = PER.rstrip('\n')
            length2 =len(PER)
            #print (length2)
            #print (line)
#           print (PER)
            C_PER  = str(line.count(PER))
#           print (C_PER)
            for R in C_PER:
                R1 = "".join(R)
                f2.write(R1+ ",")
        f2.write(val,)
        f2.write('\t')
        f2.write(line)
        f2.write('\n')
    #exit()

使用python

0 个答案: