python之如何找到一个序列中的三个字母

我有一个序列如下:

my_file_m= "TCCATTCTCTACCCAGCCCCCACTCTGACCCCTTTACTCTGACCCCTTTATTGTCTACTCCTCAGAGCCCCCAGTCTGTA 
TCCTTCTAACTTAGAAAGGGGATTATGGCTCAGGGTCCAACTCTGTGCTCAGAGCTTTCAACAACTACTCAGAAACACAA 
GATGCTGGGACAGTGACCTGGACTGTGGGCCTCTCATGCACCACCATCAAGGACTCAAATGGGCTTTCCGAATTCACTGG 
AGCCTCGAATGTCCATTCCTGAGTTCTGCAAAGGGAGAGTGGTCAGGTTGCCTCTGTCTCAGAATGAGGCTGGATAAGAT" 

我想找出具体的三个字母 TAA、TGA 和 TAG 的位置和数量。如果有的话，我想给它们上色。

我从加载字母开始

my_file = open(my_file_m) 
mine = my_file.read() 
print(mine) 

我无法使用 .count 也无法使用 find，因为我有三个输入。有什么想法如何找到它们并突出显示它们吗？

请您参考如下方法:

这是我对你问题的解答:

注意:此代码还会查找重叠序列。根据您是否要允许重叠，您必须删除 '?='

import re  
 
class bcolors: 
    HEADER = '\033[95m' 
    OKBLUE = '\033[94m' 
    OKGREEN = '\033[92m' 
    WARNING = '\033[93m' 
    FAIL = '\033[91m' 
    ENDC = '\033[0m' 
    BOLD = '\033[1m' 
    UNDERLINE = '\033[4m' 
 
my_file_m= '''TTCCATTCTCTACCCAGCCCCCACTCTGACCCCTTTACTCTGACCCCTTTATTGTCTACTCCTCAGAGCCCCCAGTCTGTATCCTTCTAACTTAGAAAGGGGATTATGGCTCAGGGTCCAACTCTGTGCTCAGAGCTTTCAACAACTACTCAGAAACACAAGATGCTGGGACAGTGACCTGGACTGTGGGCCTCTCATGCACCACCATCAAGGACTCAAATGGGCTTTCCGAATTCACTGGAGCCTCGAATGTCCATTCCTGAGTTCTGCAAAGGGAGAGTGGTCAGGTTGCCTCTGTCTCAGAATGAGGCTGGATAAGAT''' 
 
 
pat = re.compile(r'(?=(TAA|AAT|TGA|TAG))') # Very important, if you do not need overlaps then remove '?=' 
matches = re.finditer(pat,my_file_m) 
result1 = [int(match.start(1)) for match in matches] # find all the starting positions of the string 
result2 = [range(x,x+3) for x in result1 ] # find all the positions of the characters (given that we search for patterns of length 3, can be modified for other lengths too ) 
result3 = set().union(*result2) # generate a union 
 
for chari in range(len(my_file_m)): # colorize based on if it is in a sequence or not 
    if(chari in result3): 
        print bcolors.OKGREEN + my_file_m[chari]  + bcolors.ENDC, 
    else: 
        print my_file_m[chari], 

清洁工:

import re  
import sys 
 
my_file_m= '''TAATTCCATTCTCTACCCAGCCCCCACTCTGACCCCTTTACTCTGACCCCTTTATTGTCTACTCCTCAGAGCCCCCAGTCTGTATCCTTCTAACTTAGAAAGGGGATTATGGCTCAGGGTCCAACTCTGTGCTCAGAGCTTTCAACAACTACTCAGAAACACAAGATGCTGGGACAGTGACCTGGACTGTGGGCCTCTCATGCACCACCATCAAGGACTCAAATGGGCTTTCCGAATTCACTGGAGCCTCGAATGTCCATTCCTGAGTTCTGCAAAGGGAGAGTGGTCAGGTTGCCTCTGTCTCAGAATGAGGCTGGATAAGAT''' 
 
pat = re.compile(r'(?=(TAA|TGA|TAG))') # Very important, if you do not need overlaps then remove '?=' 
lettersToColor = set().union(*[range(m.start(1),m.start(1)+3) for m in re.finditer(pat, my_file_m)]) 
 
for chari in range(len(my_file_m)): # colorize based on if it is in a sequence or not 
    if(chari in lettersToColor): 
        sys.stdout.write('\033[92m' + my_file_m[chari]  +'\033[0m') 
    else: 
        sys.stdout.write(my_file_m[chari]) 

归功于:here和 here

输出: