How can I search a string for any occurrence of substring (including partial matches) in python?

Question

I am trying to write a program which will search through a series of strings and return true if any part of a substring is found.

For example, say the substring I am interested in is:

GATCGATC

The program should return True for:

GGTGGATCGATC

And should also return true for (because it ends with GATC):

GGTGTTTTGATC

So far I have:

def matchpat(str1, str2):
    '''Find a pattern in a string'''
    if str1 in str2:
        return True
    else:
        return False

This function works, but only if the whole pattern is present, it will return False for partial matches.

Partial matches with any threshold in particular? Because a matching letter is also a partial match — yatu
– yatu, Commented Mar 28, 2019 at 10:49
Please clarify your task: "any part of a substring is found" - how big the part should be? Does one letter counts as part of the string? Or do we look at the fact that "GATCGATC" is repeating of "GATC" substring? — andnik
– andnik, Commented Mar 28, 2019 at 10:55
So the sentence This is not working should also return TRUE because it ends with a substring of GATCGATC? (The sentence contains the letter G, which is a substring of GATCGATC) — Dominique
– Dominique, Commented Mar 28, 2019 at 11:01
Yes, if the string ends with a partial match, even a single G, then it should return True. — umbro_tracksuit
– umbro_tracksuit, Commented Mar 28, 2019 at 11:10

Philiong · Accepted Answer · 2019-04-18 13:36:58Z

2

Hi i made this code which works. You can change it to be more dynamical with the variables

text = 'GGTGGATCGATC'
lookingFor = 'GATCGATC'

def method():
  print('in check')
  if lookingFor in text:
    return true
  else:
    return false

def main():
  method()
  if __name__ == "__main__":

If you want to make the method take in input you can pass it in the method definition:

def method(text, lookingFor)

edited Apr 18, 2019 at 13:36

answered Mar 28, 2019 at 11:17

Philiong

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1 Comment

pyano Over a year ago

A lot of typos in the code, but it works :-). def method():, True, False, indents below def

Nick · Accepted Answer · 2019-03-28 10:55:54Z

0

I have used a library called Fuzzywuzzy for a similar problem, which worked well for my requirements and may help.

It uses Levenshtein distance metric to compare the strings.

answered Mar 28, 2019 at 10:55

Nick

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1 Comment

umbro_tracksuit Over a year ago

Thank you for your suggestion, but I wanted to try and write the code without importing any modules.

Venkataraman R · Accepted Answer · 2019-03-28 11:40:14Z

0

You can use re module to do that

import re

patterntomatch = "GATCGATC"
patterntomatch = "[{0}]".format(patterntomatch)

TextTomatch = "This is something"

matchObj = re.match(patterntomatch,TextTomatch,re.I)

if matchObj:
    print ("match found")
else:
    print("no match found")

answered Mar 28, 2019 at 11:40

Venkataraman R

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