[Bioperl-l] get regions

[Kevin Brown]

I do this in perl with the pos() function.  This requires the use of the
match operator (m) like

if ($gene =~ m/$pattern/gi)
{
	$start = pos($gene) - length($pattern) + 1;
}

pos() returns the location of the pointer where the regex left off after
finding a match.  I remove the length of my pattern (which is just a
string with a few placeholder (.) wildcards, so I know how long the
match will always be).

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Jason Stajich
> Sent: Monday, May 14, 2007 12:06 PM
> To: Thiago Venancio
> Cc: bioperl-l list
> Subject: Re: [Bioperl-l] get regions
> 
> 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
> > ========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> http://jason.open-bio.org/
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>