[Bioperl-l] get regions

[Chris Fields]

I use pos() with m{}g; the quoted globals tend to slow things down  
for me.

Ah, see Kevin's answered that...

chris

On May 14, 2007, at 2:06 PM, Jason Stajich wrote:

> 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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>> 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign