[Bioperl-l] approximate regular expression

[Adam Witney]

Hi Jose,

I've never tried it but also have a look at this module:

http://search.cpan.org/~limaone/Bio-Grep-v0.10.6/lib/Bio/Grep.pm

Adam

On 22 Mar 2012, at 20:47, José Ramón Blas Pastor wrote:

> I want to find all the matches of a given pattern in a string but doing
> fuzzy (approximate) pattern matching. I want to allow small variations (1
> or 2 positions substituted) in the match. I have tried String::approx
> module, but I do not know how to manage syntax
> 
> ...
> use String::approx 'amatch';
> my $pattern = "JEJE";
> my $string = "EJKJUJHJDJEJEJEDEJOJOJJJAHJHJSHJEFEJUJEJUJKIJS";
> while (?=/$pattern/) {
> ...
> [download] <http://perlmonks.org/index.pl?abspart=1;displaytype=displaycode;node_id=961099;part=1>
> 
> How could I achieve that this 'while' allow 1 substitution from $pattern?
> That is that "JEFE", "JUJE","JEDE",... would be true matches.
> 
> Thanks a lot in advance. JR
> 
> -- 
> José Ramón Blas - PhD
> Dept. Biochemistry - Medicine School
> University of Castilla-La Mancha
> C Almansa, 14
> 02006 Albacete (Spain)
> 
> Phone: +34 967599200 ext. 2958
> 
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