Aziz,
I guess I hadn't thought about it that way, so here is more info.
What I'm basically doing is randomly pulling a string of 500 from one string
and looking for it in another string. So I'm looking for a substring of the
larger string that matches my query string. In terms of how it matches the
answer and to your questions, all of the above. I don't care if there are
insertions, deletions of just character changes, as long as the query sting is
80% similar to the subject string.
Like I said I know I can use the module Similarity. But in order to do this I
would need bot the query and the subject string. And to get the subject string
I would need to 'slide' down the larger string and pull out all combinations 1
by 1. This is very slow with a 4.5 million character string. I'm just looking
for a way to speed things up.
BTW, if it helps at all, I'm doing genetic analysis of whole genomes, hence the
4.5 million long string.
-Bob
--- Abdulaziz Ghuloum <[EMAIL PROTECTED]> wrote:
> Hello,
>
> I don't have a direct answer for your question since your question is a
> little bit ambigious; let me explain:
>
> Do you want to search for a substring in a long string, or you want true
> regexp match?
>
> If you want a true regexp match, then the question is even more
> ambigious. For example, the regexp /(ab){20}a{10}/ does not match the
> string "ababababababaaaaaaaaa", but what percentage does it match? How
> do you determine the percentage let alone matching for a given error
> percentage.
>
> If you just want a substring match (not a regexp), then your problem is
> simpler, but you need to define your criteria more clearly.
>
> Do you want to allow up to 20% more characters to be inserted to the
> substring and still consider it a match?
>
> Do you want to match down to 80% of the substring and still consider it a
> match?
>
> Do you want to allow up to 20% of the characters to be altered (not
> removed or inserted) and still consider it a match?
>
> Or a combination of the above?
>
> Without this information, no reply is even remotely correct. Please
> provide more information about the problem to get closer to the solution
> to your problem.
>
> Hope this helps,,,
>
> Aziz,,,
>
> In article <[EMAIL PROTECTED]>, "Bob
> Mangold" <[EMAIL PROTECTED]> wrote:
>
> > Hello,
> >
> > I'm working on a program where I am searching for a short string within
> > a longer string. The catch is that the long string is about 4.5 million
> > chars long and the short string is about 500. Using a regex to do an
> > exact match is simple, but what if I want just a close match, like 80%
> > or whatever. I've used the module Similarity in the past, but in order
> > to use that I have to send it two string to compare, which means I'd
> > have to slide down the longer string character by character. Is there a
> > faster way. Is there a module that returns true for a regex match within
> > a certain percentage?
> >
> > -Bob
> >
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