Function that returns in a list the positions where the motif was found in a sequence

Question

I have these two strings:

 t = 'GATATCATGCATATACTT'
 s = 'ATAT'

I am trying to create a function that returns in a list the positions where the reason for the string s was found in the sequence of the string t. That is, in this case, the positions would be [1, 10]. But also, if the reason is not found, the list will return [-1].

 def search_motif (t, s):
     search_motif = list()
     for i, x in enumerate(t):
         if s in x:
             search_motif.append(i)
     i + = 1

     return [-1] # this must go to the end

 print (search_motif (t, s))

Am I going the right way? Can someone please guide me?

Clearly your function is not returning results. Have you run it in a debugger? — Mad Physicist, Dec 19 '21 at 02:16
You are starting correctly, but you are not using the loop correctly. What is `x` in the loop? You are not returning the list you generate if it's not empty. I recommend something like `return search_motif or [-1]` — Mad Physicist, Dec 19 '21 at 02:17
Here's your duplicate: https://stackoverflow.com/q/4664850/2988730 — Mad Physicist, Dec 19 '21 at 03:04

BG Park · Accepted Answer · 2021-12-19T03:09:25.190

2

Using regular expressions seems to be a better way.

import re

def search_motif(t, s):
    p = re.compile(s)
    motif = []
    for mo in p.finditer(t):
        motif.append(mo.start())
    
    if motif:
        return motif
    else:
        return -1

Edit: mo.span()[0] --> mo.start()

edited Dec 19 '21 at 03:09

answered Dec 19 '21 at 02:33

BG Park

169
7

Copperfield · Answer 2 · 2021-12-19T02:42:59.820

You can use str.index for this

>>> def findall(text,subtext):
        i=0
        ind=[]
        while True:
            try:
                i = text.index(subtext,i) #the second argument tell where to start looking for the sub string
                ind.append(i)
                i +=1 #for the next iteration we start looking in the immediate next index
            except ValueError: #we break when no more occurrences are found 
                break 
        if i==0: #we check if we didn't found a match before
            ind.append(-1)
        return ind

        
>>> t = 'GATATCATGCATATACTT'
>>> s = 'ATAT'
>>> findall(t,s)
[1, 10]
>>> findall(t,"X")
[-1]
>>>

Now about your code, there are 2 reason it doesn't work: the first is that you don't return the list you make and the second is because you are looking at the individual characters

>>> for i,x in enumerate("HELLO"):
    print(x)

    
H
E
L
L
O
>>>

and if you aren't searching for a character you would never get a match

Function that returns in a list the positions where the motif was found in a sequence

2 Answers2