[Bioperl-l] get regions

[aaron.j.mackey at gsk.com]

Or, use a zero-width, positive look ahead assertion, and don't incur the 
penalty of either $` or $&:

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

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 05/14/2007 09:46:55 PM:

> On 5/14/07, Kevin Brown <Kevin.M.Brown at asu.edu> wrote:
> > 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($pattern) + 1;
> > }
> >
> > pos() returns the location of the pointer where the regex left off 
after
> > finding a match.
> 
> Cool. I hadn't known that was possible.
> 
> > I remove the length of my pattern (which is just a
> > string with a few placeholder (.) wildcards, so I know how long the
> > match will always be).
> 
> To generalize your code so that it will work for any pattern, such as
> one that can match strings of variable length like "A{5,10}", just
> subtract the length of the actual string that was matched:
> 
> if ($gene =~ m/$pattern/gi)
> {
>     $start = pos($gene) - length($&) + 1;
>  }
> 
> Steve
> 
> > > -----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/
> > >
> > >
> > > _______________________________________________
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> > > Bioperl-l at lists.open-bio.org
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> > >
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