From: Harry Kakueki <list.push@...>
Date: 2010-09-22T21:47:31+09:00
Subject: Re: Search for a string in another string allowing mismatches

On Wed, Sep 22, 2010 at 3:07 AM, Janus Bor <janus@urban-youth.com> wrote:
>
> Basically, I want to find out if a string contains my search string as a
> substring. However, a certain amount of mismatches has to be allowed.
> Here's an example:
>
> query string:
> "acgt"
>
> subject string
> "acctaggg"
>
> If no mismatch was allowed, there would be 0 hits.
> If 1 mismatch was allowed, the query string would match "acct".
> If 2 mismatches were allowed, the query string would match "acct" and
> "aggg".
>

This does not use regular expressions.
It does not tell you which characters match. It tells you how many.

I don't know if it is useful or fast enough but maybe it will give you
some ideas.


str = "acctaggg"

(0..str.length-4).each do |y|
  p str.unpack("@#{y}a4")[0].split(//).zip("acgt".split(//)).map{|r|
r[0]<=>r[1]}.select{|f| f==0}.size
end



Harry