[Bioperl-l] get regions

[Jason Stajich]

I assume you are doing the matches on the string with =~ so Bio::Seq  
doesn't really help you here I don't think.
See the $` variable in Perl for how to capture the position of where  
a regexp matches.

-jason
On May 14, 2007, at 11:54 AM, Thiago Venancio wrote:

> Hi all,
>
> Using Bio::Seq, is there any easy way to get the coordinates where a
> regular expression matches or should I build a sliding window?
>
> For example, looking for a given promoter region in a FASTA file. If
> the region is found, I would like to recover exactly the coordinates
> where it matches.
>
> Thanks in advance.
>
> Thiago
> -- 
> "Doubt is not a pleasant condition, but certainty is absurd."
>             Voltaire
>
> ========================
> Thiago Motta Venancio, MSc
> PhD student in Bioinformatics
> University of Sao Paulo
> ========================
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--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/