[Bioperl-l] Writing bp_grep

[Fields, Christopher J]

Bio::Tools::SeqPattern could be used (and improved upon if needed) for pattern generation. 

chris

On May 13, 2012, at 12:36 PM, Hilmar Lapp wrote:

> And of course there's tacg (though I have never used it - not sure about its status):
> 
> Mangalam HJ (2002) tacg – a grep for DNA. BMC Bioinformatics 3:8
> doi:10.1186/1471-2105-3-8
> 
> 	-hilmar
> 
> On May 13, 2012, at 1:26 PM, Peter Cock wrote:
> 
>> On Sunday, May 13, 2012, Carnë Draug wrote:
>> 
>>> Hi everyone
>>> 
>>> I'm starting to write a grep tool for sequences (bp_grep). The idea is
>>> to have something just like grep but for DNA and protein sequences
>>> with most of the options that make sense in this context (print the
>>> filename or sequence name only, position, without match search, count,
>>> etc). I was wondering if anyone has any piece of code that could fit
>>> in it or started something similar but just never finished.
>>> 
>>> Thanks,
>>> Carnë
>>> 
>> 
>> This sounds like EMBOSS preg,
>> http://emboss.open-bio.org/wiki/Appdoc:Preg
>> 
>> I thought they had a nucleotide equivalent but I can't see
>> it right now....
>> 
>> Peter
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
> 
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l