[Tutor] finding a polymer of letters in a string

[Hs Hs]

Hi Hilton. Thanks for your suggestion. 



I saw re module. I should have explain a little bit in my message that patter of polymer is not constant. There could be variety of combinations given A, T G and C. 

it could be AAATAAA, ATATATAT, or GTAGTAGTA or GGGACCCGAAAT etc.


so I do not know what that pattern would be when I read in a string. I do not know if regex could solve my kind of problem too. 


Thanks
Hs.





________________________________
 From: Hilton Fernandes <hgfernan at gmail.com>
To: "tutor at python.org" <tutor at python.org> 
Cc: Hs Hs <ilhs_hs at yahoo.com> 
Sent: Thursday, January 19, 2012 1:39 PM
Subject: Re: [Tutor] finding a polymer of letters in a string
 

Hi ! 

Have you considered regular expressions in Python ? 

Please take a look at "Regular Expression HOWTO", at 
http://docs.python.org/howto/regex.html

All the best, 
Hilton 


On Thu, Jan 19, 2012 at 4:09 PM, Hs Hs <ilhs_hs at yahoo.com> wrote:

Hi: 
>I am writing to see if I could any help.
>I am trying to find if a mutation in gene falls in a polymer region of DNA. To explain in simplistic terms, 
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>Given a piece of DNA string, with following characters, I know where mutation happens.  Happens at T (in quotes with spaces.) 3 As before T and 4 As after T are removed in a disease. 
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>Given following sequence, I should be able to find if this T is in a polymer region. such as 'AAA' T 'AAAA. 
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>AAATAGCAGAAA 'T' AAAAGAAAAGATTGGAACTAGGTCAG
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>I am not sure if there are any methods in python to find these.  Do you think a script has to be written with more logic involving some known algorithms. 
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>Please advise. 
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>thanksHs.
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