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

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1

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.

python python-3.x

share|improve this question

asked Mar 28 at 10:47

umbro_tracksuitumbro_tracksuit

2655 bronze badges

• 
  
  
  

  
  2
  

  
  
  
  
  
  

  
  
  Partial matches with any threshold in particular? Because a matching letter is also a partial match
  
  – yatu
  Mar 28 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
  Mar 28 at 10:55
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Please post a sample for both True and False cases.
  
  – DirtyBit
  Mar 28 at 10:57
  

  
  
  
  


• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  
  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
  Mar 28 at 11:01
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Yes, if the string ends with a partial match, even a single G, then it should return True.
  
  – umbro_tracksuit
  Mar 28 at 11:10
  

  
  
  
  

 | 
show 3 more comments

1

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.

python python-3.x

share|improve this question

asked Mar 28 at 10:47

umbro_tracksuitumbro_tracksuit

2655 bronze badges

• 
  
  
  

  
  2
  

  
  
  
  
  
  

  
  
  Partial matches with any threshold in particular? Because a matching letter is also a partial match
  
  – yatu
  Mar 28 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
  Mar 28 at 10:55
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Please post a sample for both True and False cases.
  
  – DirtyBit
  Mar 28 at 10:57
  

  
  
  
  


• 
  
  
  

  
  1
  

  
  
  
  
  
  

  
  
  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
  Mar 28 at 11:01
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Yes, if the string ends with a partial match, even a single G, then it should return True.
  
  – umbro_tracksuit
  Mar 28 at 11:10
  

  
  
  
  

 | 
show 3 more comments

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.

python python-3.x

share|improve this question

asked Mar 28 at 10:47

umbro_tracksuitumbro_tracksuit

2655 bronze badges

GATCGATC

GGTGGATCGATC

GGTGTTTTGATC

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

share|improve this question

asked Mar 28 at 10:47

umbro_tracksuitumbro_tracksuit

2655 bronze badges

share|improve this question

asked Mar 28 at 10:47

umbro_tracksuitumbro_tracksuit

2655 bronze badges

asked Mar 28 at 10:47

umbro_tracksuitumbro_tracksuit

2655 bronze badges

asked Mar 28 at 10:47

umbro_tracksuitumbro_tracksuit

2655 bronze badges

3 Answers
3

active

oldest

votes

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)

share|improve this answer

edited Apr 18 at 13:36

answered Mar 28 at 11:17

Phillip EismarkPhillip Eismark

2144 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  A lot of typos in the code, but it works :-). def method():, True, False, indents below def
  
  – pyano
  Apr 12 at 17:11
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Haha sorry and thanks!
  
  – Phillip Eismark
  Apr 18 at 13:36
  

  
  
  
  

add a comment
 | 

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.

share|improve this answer

answered Mar 28 at 10:55

NickNick

1,52322 gold badges1818 silver badges3737 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thank you for your suggestion, but I wanted to try and write the code without importing any modules.
  
  – umbro_tracksuit
  Mar 28 at 11:10
  

  
  
  
  

add a comment
 | 

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")

share|improve this answer

answered Mar 28 at 11:40

Venkataraman RVenkataraman R

2,4511111 silver badges2020 bronze badges

add a comment
 | 

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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)

share|improve this answer

edited Apr 18 at 13:36

answered Mar 28 at 11:17

Phillip EismarkPhillip Eismark

2144 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  A lot of typos in the code, but it works :-). def method():, True, False, indents below def
  
  – pyano
  Apr 12 at 17:11
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Haha sorry and thanks!
  
  – Phillip Eismark
  Apr 18 at 13:36
  

  
  
  
  

add a comment
 | 

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)

share|improve this answer

edited Apr 18 at 13:36

answered Mar 28 at 11:17

Phillip EismarkPhillip Eismark

2144 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  A lot of typos in the code, but it works :-). def method():, True, False, indents below def
  
  – pyano
  Apr 12 at 17:11
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Haha sorry and thanks!
  
  – Phillip Eismark
  Apr 18 at 13:36
  

  
  
  
  

add a comment
 | 

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)

share|improve this answer

edited Apr 18 at 13:36

answered Mar 28 at 11:17

Phillip EismarkPhillip Eismark

2144 bronze badges

text = 'GGTGGATCGATC'
lookingFor = 'GATCGATC'

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

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

def method(text, lookingFor)

share|improve this answer

edited Apr 18 at 13:36

answered Mar 28 at 11:17

Phillip EismarkPhillip Eismark

2144 bronze badges

answered Mar 28 at 11:17

Phillip EismarkPhillip Eismark

2144 bronze badges

answered Mar 28 at 11:17

Phillip EismarkPhillip Eismark

2144 bronze badges

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.

share|improve this answer

answered Mar 28 at 10:55

NickNick

1,52322 gold badges1818 silver badges3737 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thank you for your suggestion, but I wanted to try and write the code without importing any modules.
  
  – umbro_tracksuit
  Mar 28 at 11:10
  

  
  
  
  

add a comment
 | 

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.

share|improve this answer

answered Mar 28 at 10:55

NickNick

1,52322 gold badges1818 silver badges3737 bronze badges

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Thank you for your suggestion, but I wanted to try and write the code without importing any modules.
  
  – umbro_tracksuit
  Mar 28 at 11:10
  

  
  
  
  

add a comment
 | 

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.

share|improve this answer

answered Mar 28 at 10:55

NickNick

1,52322 gold badges1818 silver badges3737 bronze badges

share|improve this answer

answered Mar 28 at 10:55

NickNick

1,52322 gold badges1818 silver badges3737 bronze badges

answered Mar 28 at 10:55

NickNick

1,52322 gold badges1818 silver badges3737 bronze badges

answered Mar 28 at 10:55

NickNick

1,52322 gold badges1818 silver badges3737 bronze badges

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")

share|improve this answer

answered Mar 28 at 11:40

Venkataraman RVenkataraman R

2,4511111 silver badges2020 bronze badges

add a comment
 | 

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")

share|improve this answer

answered Mar 28 at 11:40

Venkataraman RVenkataraman R

2,4511111 silver badges2020 bronze badges

add a comment
 | 

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")

share|improve this answer

answered Mar 28 at 11:40

Venkataraman RVenkataraman R

2,4511111 silver badges2020 bronze badges

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")

share|improve this answer

answered Mar 28 at 11:40

Venkataraman RVenkataraman R

2,4511111 silver badges2020 bronze badges

answered Mar 28 at 11:40

Venkataraman RVenkataraman R

2,4511111 silver badges2020 bronze badges

answered Mar 28 at 11:40

Venkataraman RVenkataraman R

2,4511111 silver badges2020 bronze badges